Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,885,012	C→T	P66L (CCT→CTT)	yidD →	membrane protein insertion efficiency factor

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,885,012	0	C	T	96.9%	105.6 / NA	32	P66L (CCT→CTT)	yidD	membrane protein insertion efficiency factor
Reads supporting (aligned to +/- strand):  ref base C (0/0);  major base T (20/11);  minor base G (0/1);  total (20/12)
Fisher's exact test for biased strand distribution p-value = 3.75e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.82e-01

GTTGCCGACCTCGATAACCGTGCTCTCTCGGAAGCGTTGGAAAAATTATGGCGCCGCCACTGTCGCCTGGCTCGCGGGTCCTGATAGCCCTCATTCGGGTCTATCAACGCCTGATTAGTCCGCTACTCGGGCCGCATTGTCGTTTCACTCCAACCTGTTCAAGCTACGGAATTGAGGCATTGCGCAGGTTTGGAGTGATAAAAGGCAGTTGGTTGACGGTGAAACGCGTATTAAAATGCCACCCTTTACACCCTGGTGGTGACGATCCCGTCCCGCCCGGACCATTTGATACCAGAGAACACTAACGATGGATTCGCAACGCAATCTTTTAGTCATCGCTTTGCTGTTCGTGTCTTTCATGATCTGGCAAGCCTGGGAGCAGGATAAAAACCCGCAACCTCAGGCCCAACAGACCACGCAGACAACGACCACCGCAGCGGGTAGCGCCGCCGACCAGGGCGTACCGGCCAGTGGCCAGGGGAAAC  >  NC_000913/3884769‑3885253                                                                                                                                                                                                                                                    |                                                                                                                                                                                                                                                  gTTGCCGCCCTCGATAGCCTTGCTCTCTCGGAAGCTTTGAAAAAATTATGGCGCCGCCACTTTCGCCTGGCTCGCGGGTCCTGATAGCCCTCAGTCGGGTCTATCAACGCCTTATTAGTCCGCTACTCGGGCCGCATTGTCGTTTCACTCCAACCTGTGCAAGCTACGGAATTGAGGCATTGCGCAGGTTTGGAGTGATAAAATGCAGTTGGTTGACGGTGAAACGCGTATTAAAATGCCACCTTTTacac                                                                                                                                                                                                                                            <  1:254697/251‑1 (MQ=255)  ttGCCGACCTCGATAACCGTGCTCTCTCGGAAGCGTTGGAAAAATTATGGCGCCGCCACTGTCGCCTGGCTCGCGGGTCCTGATAGCCCTCATTCGGGTCTATCAACGCCTGATTAGTCCGCTACTCGGGCCGCATTGTCGTTTCACTCCAACCTGTTCAAGCTACGGAATTGAGGCATTGCGCAGGTTTGGAGTGATAAAAGGCAGTTGGTTGACGGTGAAACGCGTATTAAAATGCCACCTTTTACAcc                                                                                                                                                                                                                                           >  2:80005/1‑251 (MQ=255)   tGCCGACCTCGATAACCGTGCTCTCTCGGAAGCGTTGGAAAAATTATGGCGCCGCCACTGTCGCCTGGCTCGCGGGTCCTGATAGCCCTCATTCGGGTCTATCAACGCCTGATTAGTCCGCTACTCGGGCCGCATTGTCGTTTCACTCCAACCTGTTCAAGCTACGGAATTGAGGCATTGCGCAGGTTTGGAGTGATAAAAGGCAGTTGGTTGACGGTGAAACGCGTATTAAAATGCCACCTTTTACAccc                                                                                                                                                                                                                                          >  1:238982/1‑251 (MQ=255)            cGATAACCGTGCTCTCTCGGAAGCGTTGGAAAAATTATGGCGCCGCCACTGTCGCCTGGCTCGCGGGTCCTGATAGCCCTCATTCGGGTCTATCAACGCCTGATTAGTCCGCTACTCGGGCCGCATTGTCGTTTCACTCCAACCTGTTCAAGCTACGGAATTGAGGCATTGCGCAGGTTTGGAGTGTTAAAAGGCAGTTGGTTGACGGTGAAAAGCGTATTAAAATGCCACCTTTTACACCCTGgtggtg                                                                                                                                                                                                                                  >  2:250254/1‑250 (MQ=255)            cGATAACCGTGCTCTCTCGGAAGCGTTGGAAAAATTATGGCGCCGCCACTGTCGCCTGGCTCGCGGGTCCTGATAGCCCTCATTCGGGTCTATCAACGCCTGATTAGTCCGCTACTCGGGCCGCATTGTCGTTTCACTCCAACCTGTTCAAGCTACGGAATTGAGGCATTGCGCAGGTTTGGAGTGATAAAAGGCAGTTGGTTGACGGTGAAACGCGTATTAAAATGCCACCTTTTACACCCTGgtggtg                                                                                                                                                                                                                                  >  2:43760/1‑250 (MQ=255)              aTAACCGTGCTCTCTCGGAAGCGTTGGAAAAATTATGGCGCCGCCACTGTCGCCTGGCTCGCGGGTCCTGATAGCCCTCATTCGGGTCTATCAACGCCTGATTAGTCCGCTACTCGGGCCGCATTGTCGTTTCACTCCAACCTGTTCAAGCTACGGAATTGAGGCATTGCGCAGGTTTGGAGTGATAAAAGGCAGTTGGTTGACGGTGAAACGCGTATTAAAATGCCACCTTTTACACCCTGGTGGTGACg                                                                                                                                                                                                                               >  1:252745/1‑251 (MQ=255)                               gAAGCGTTGGAAAAATTATGGCGCCGCCACTGTCGCCTGGCTCGCGGGTCCTGATAGCCCTCATTCGGGTCTATCAACGCCTGATTAGTCCGCTACTCGGGCCGCATTGTCGTTTCACTCCAACCTGTTCAAGCTACGGAATTGAGGCATTGCGCAGGTTTGGAGTGATAAAAGGCAGTTGGTTGACGGTGAAACGCGTATTAAAATGCCACCTTTTACACCCTGGTGGTGACGATCCCGTCCCGCCCggc                                                                                                                                                                                                              >  2:106373/1‑250 (MQ=255)                                           aaaTTAGGGCCCCGCCACTGTGGCCTGGCTCGCGGGTCCTGATAGCCCTCAGTCGGGTCTATCAACGCCTGATTAGTCCGCTACTCGGGCCGCATTGTCGTTTCACTCCAACCTGTTCAAGCTACGGAATTGAGGCATTGCGCAGGTGTGGAGTGATAAAAGGCAGTTGGTTTACGGTGAAACGCGTATTAAAATGCCACCGTTTACACCCGGGTGGTGACGATGGCGTCCCGCCCGGACCATTTGATAcc                                                                                                                                                                                                  <  2:110281/251‑1 (MQ=255)                                                aTGGCGCCGCCACTGTCGCCTGGCTCGCGGGTCCTGATAGCCCTCATTCGGGTCTATCAACGCCTGATTAGTCCGCTACTCGGGCCGCATTGTCGTTTCACTCCAACCTGTTCAAGCTACGGAATTGAGGCATTGCGCAGGTTTGGAGTGATAAAAGGCAGTTGGTTGACGGTGAAACGCGTATTAAAATGCCACCTTTTACACCCTGGTGGTGACGATCCCGTCCCGCCCGGACCATTTGATACCag                                                                                                                                                                                                >  2:158016/1‑248 (MQ=255)                                                                     ggCTCGCGGGTCCTGATAGCCCTCATTCGGGTCTATCAACGCCTGATTAGTCCGCTACTCGGGCCGCATTGTCGTTTCACTCCAACCTGTTCAAGCTACGGAATTGAGGCATTGCGCAGGTTTGGAGTGATAAAAGGCAGTTGGTTGACGGTGAAACGCGTATTAAAATGCCACCTTTTACACCCTGGTGGTGACGATCCCGTCCCGCCCGGACCATTTGATACCAGAGAACACTAACGATGGATTcgcaa                                                                                                                                                                        <  1:236821/251‑1 (MQ=255)                                                                     ggCTCGCGGGTCCTGATAGCCCTCATTCGGGTCTATCAACGCCTGATTAGTCCGCTACTCGGGCCGCATTGTCGTTTCACTCCAACCTGTTCAAGCTACGGAATTGAGGCATTGCGCAGGTTTGGAGTGATAAAAGGCAGTTGGTTGACGGTGAAACGCGTATTAAAATGCAACCTTTTACACCCTGGTGTTGACGATCCCGTCCCGCCCGGACCATTTGATACCAGAGAACACTAACGATGGATTcgca                                                                                                                                                                         >  2:73528/1‑250 (MQ=255)                                                                                                 gggTCTATCAACGCCTGATTAGTCCGCTACTCGGGCCGCATTGTCGTTTCACTCCAACCTGTTCAAGCTACGGAATTGAGGCATTGCGCAGGTTTGGAGTGATAAAAGGCAGTTGGTTGACGGTGAAACGCGTATTAAAATGCCACCTTTTACACCCTGGTGGTGACGATCCCGTCCCGCCCGGACCATTTGATACCAGAGAACACTAACGATGGATTCGCAACGCAATCTTTTAGTCATCGCTTTGCTGt                                                                                                                                            <  1:158016/251‑1 (MQ=255)                                                                                                                     aGTCCGCTACTCGGGCCGCATTGTCGTTTCACTCCAACCTGTTCAAGCTACGGAATTGAGGCATTGCGCAGGTTTGGAGTGATAAAAGGCAGTTGGTTGACGGTGAAACGCGTATTAAAATGCCACCTTTTACACCCTGGTGGTGACGATCCCGTCCCGCCCGGACCATTTGATACCAGAGAACACTAACGATGGATTCGCAACGCAATCTTTTAGTCATCGCTTTGCTGTTCGTGTCTTTCATGATCTg                                                                                                                         <  2:130923/250‑1 (MQ=255)                                                                                                                         cGCTACTCGGGCCGCATTGTCGTTTCACTCCAACCTGTTCAAGCTACGGAATTGAGGCATTGCGCAGGTTTGGAGTGATAAAAGGCAGTTGGTTGACGGTGAAACGCGTATTAAAATGCCACCTTTTACACCCTGGTGGTGACGATCCCGTCCCGCCCGGACCATTTGATACCAGAGAACACTAACGATGGATTCGCAACGCAATCTTTTAGTCATCGCTTTGCTGTTCGTGTCTTTCATGATCTGGCAAg                                                                                                                    <  1:222644/251‑1 (MQ=255)                                                                                                                                       cATTGTCGTTTCACTCCAACCTGTTCAAGCTACGGAATTGAGGCATTGCGCAGGTTTGGAGTGATAAAAGGCAGTTGGTTGACGGTGAAACGCGTATTAAAATGCCACCTTTTACACCCTGGTGGTGACGATCCCGTCCCGCCCGGACCATTTGATACCAGAGAACACTAACGATGGATTCGCAACGCAATCTTTTAGTCATCGCTTTGCTGTTCGTGTCTTTCATGATCTGGCAAGCCTGGGAGCAGGAt                                                                                                      <  1:80005/251‑1 (MQ=255)                                                                                                                                       cATTGTCGTTTCACTCCAACCTGTTCAAGCTACGGAATTGAGGCATTGCGCAGGTTTGGAGTGATAAAAGGCAGTTGGTTGACGGTGAAACGCGTATTAAAATGCCACCTTTTACACCCTGGTGGTGACGATCCCGTCCCGCCCGGACCATTTGATACCAGAGAACACTAACGATGGATTCGCAACGCAATCTTTTAGTCATCGCTTTGCTGTTCGTGTCTTTCATGATCTGGCAAGCCTGGGAGCAGGAt                                                                                                      >  2:63050/1‑251 (MQ=255)                                                                                                                                           gTCGTTTCACTCCAACCTGTTCAAGCTACGGAATTGAGGCATTGCGCAGGTTTGGAGTGATAAAAGGCAGTTGGTTGACGGTGAAACGCGTATTAAAATGCCACCTTTTACACCCTGGTGGTGACGATCCCGTCCCGCCCGGACCATTTGATACCAGAGAACACTAACGATGGATTCGCAACGCAATCTTTTAGTCATCGCTTTGCTGTTCGTGTCTTTCATGATCTGGCAAGCCTGGGAGCAGGATaaa                                                                                                   >  1:173914/1‑250 (MQ=255)                                                                                                                                                      ccAACCTGTTCAAGCTACGGAATTGAGGCATTGCGCAGGTTTGGAGTGATAAAAGGCAGTTGGTTGACGGTGAAACGCGTATTAAAATGCCACCTTTTACACCCTGGTGGTGACGATCCCGTCCCGCCCGGACCATTTGATACCAGAGAACACTAACGATGGATTCGCAACGCAATCTTTTAGTCATCGCTTTGCTGTTCGTGTCTTTCATGATCTGGCAAGCCTGGGAGCAGGATAAAAACCCGCAACCt                                                                                       <  1:25528/251‑1 (MQ=255)                                                                                                                                                       cAACCTGTTCAAGCTACGGAATTGAGGCATTGCGCAGGTTTGGAGTGATAAAAGGCAGTTGGTTGACGGTGAAACGCGTATTAAAATGCCACCTTTTACACCCTGGTGGTGACGATCCCGTCCCGCCCGGACCATTTGATACCAGAGAACACTAACGATGGATTCGCAACGCAATCTTTTAGTCATCGCTTTGCTGTTCGTGTCTTTCATGATCTGGCAAGCCTGGGAGCAGGATAAAAACCCGCAACCTc                                                                                      >  1:199967/1‑251 (MQ=255)                                                                                                                                                             gTTCAAGCTACGGAATTGAGGCATTGCGCAGGTTTGGAGTGATAAAAGGCAGTTGGTTGACGGTGAAACGCGTATTAAAATGCCACCTTTTACACCCTGGTGGTGACGATCCCGTCCCGCCCGGACCATTTGATACCAGAGAACACTAACGATGGATTCGCAACGCAATCTTTTAGTCATCGCTTTGCTGTTCGTGTCTTTCATGATCTGGCAAGCCTGGGAGCAGGATAAAAACCCGCAACCTCAGGcc                                                                                 <  1:246121/250‑1 (MQ=255)                                                                                                                                                                  aGCTACGGAATTGAGGCATTGCGCAGGTTTGGAGTGATAAAAGGCAGTTGGTTGACGGTGAAACGCGTATTAAAATGCCACCTTTTACACCCTGGTGGTGACGATCCCGTCCCGCCCGGACCATTTGATACCAGAGAACACTAACGATGGATTCGCAACGCAATCTTTTAGTCATCGCTTTGCTGTTCGTGTCTTTCATGATCTGGCAAGCCTGGGAGCAGGATAAAAACCCGCAACCTCAGGCCCAAc                                                                             >  1:124136/1‑249 (MQ=255)                                                                                                                                                                           aTTGAGGCATTGCGCAGGTTTGGAGTGATAAAAGGCAGTTGGTTGACGGTGAAACGCGTATTAAAATGCCACCTTTTACACCCTGGTGGTGACGATCCCGTCCCGCCCGGACCATTTGATACCAGAGAACACTAACGATGGATTCGCAACGCAATCTTTTAGTCATCGCTTTGCTGTTCGTGTCTTTCATGATCTGGCAAGCCTGGGAGCAGGATAAAAACCCGCAACCTCAGGCCCAACAGACCACGc                                                                    >  1:34335/1‑249 (MQ=255)                                                                                                                                                                               aGGCATTGCGCAGGTTTGGAGTGATAAAAGGCAGTTGGTTGACGGTGAAACGCGTATTAAAATGCCACCTTTTACACCCTGGTGGTGACGATCCCGTCCCGCCCGGACCATTTGATACCAGAGAACACTAACGATGGATTCGCAACGCAATCTTTTAGTCATCGCTTTGCTGTTCGTGTCTTTCATGATCTGGCAAGCCTGGGAGCAGGATAAAAACCCGCAACCTCAGGCCCAACAGACCACGCAGNCa                                                               >  2:259639/1‑250 (MQ=255)                                                                                                                                                                                 gCATTGCGCAGGTTTGGAGTGATAAAAGGCAGTTGGTTGACGGTGAAACGCGTATTAAAATGCCACCTTTTACACCCTGGTGGTGACGATCCCGTCCCGCCCGGACCATTTGATACCAGAGAACACTAACGATGGATTCGCAACGCAATCTTTTAGTCATCGCTTTGCTGTTCGTGTCTTTCATGATCTGGCAAGCCTGGGAGCAGGATAAAAACCCGCAACCTCAGGCCCAACAGACCACGCAGACAACg                                                            >  1:218188/1‑251 (MQ=255)                                                                                                                                                                                                 gAGTGATAAAAGGCAGTTGGTTGACGGTGAAACGCGTATTAAAATGCCACCTTTTACACCCTGGTGGTGACGATCCCGTCCCGCCCGGACCATTTGATACCAGAGAACACTAACGATGGATTCGCAACGCAATCTTTTAGTCATCGCTTTGCTGTTCGTGTCTTTCATGATCTGGCAAGCCTGGGAGCAGGATAAAAACCCGCAACCTCAGGCCCAACAGACCACGCAGACAACGACCACCGCAGCGGGt                                             >  1:195703/1‑250 (MQ=255)                                                                                                                                                                                                            ggCAGTTGGTTGACGGTGAAACGCGTATTAAAATGCCACCTTTTACACCCTGGTGGTGACGATCCCGTCCCGCCCGGACCATTTGATACCAGAGAACACTAACGATGGATTCGCAACGCAATCTTTTAGTCATCGCTTTGCTGTTCGTGTCTTTCATGATCTGGCAAGCCTGGGAGCAGGATAAAAACCCGCAACCTCAGGCCCAACAGACCACGCAGACAACGACCACCGCAGCGGGTAGCGCCGCCGAc                                 >  1:72797/1‑251 (MQ=255)                                                                                                                                                                                                               aGTTGGTTGGCGGTGAAACGCGTATTAAAATGCCACCTTTTACACCCTGGTGGTGACGATCCCGTCCCGCCCGGACCATTTGATACCAGAGAACACTAACGATGGATTCGCAACGCAATCTTTTAGTCATCGCTTTGCTGTTCGTGTCTTTCATGATCTGGCAAGCCTGGGAGCAGGATAAAAACCCGCAACCTCAGGCCCAACAGACCACGCAGACAACGACCACCGCAGCGGGTAGCGCCGCCGACCAg                              <  2:195703/251‑1 (MQ=255)                                                                                                                                                                                                                          ggTGAAACTCGTATTAAAATGCCACCTTTTACACCCTGGTGGTGACGATCCCGTCCCGCCCGGACCATTTGATACCAGAGAACACTAACGATGGATTCGCAACGCAATCTGTTAGTCATCGCTTTGCTGTTCGTGTCTTTCATGATCTGGCAAGCCTGGGAGCAGGATAAAAACCCGCAACCTCAGGCCCAACAGACCACGCAGACAACGACCACCGCAGCGGGTAGCGCCGCCGACCAGGTCGTACCGGc                   >  2:27679/1‑251 (MQ=255)                                                                                                                                                                                                                             gAAACGCGTATTAAAATGCCACCTTTTACACCCTGGTGGTGACGATCCCGTCCCGCCCGGACCATTTGATACCAGAGAACACTAACGATGGATTCGCAACGCAATCTTTTAGTCATCGCTTTGCTGTTCGTGTCTTTCATGATCTGGCAAGCCTGGGAGCAGGATAAAAACCCGCACCCTCAGGCCCAACAGACCACGCAGACAACGACCACCGCAGCGGGTAGCGCCGCCGACCAGGGCGTACCGGCCAg                <  2:221568/251‑1 (MQ=255)                                                                                                                                                                                                                               aaCGCGTATTAAAATGCCACCTTTTACACCCTGGTGGTGACGATCCCGTCCCGCCCGGACCATTTGATACCAGAGAACACTAACGATGGATTCGCAACGCAATCTTTTAGTCATCGCTTTGCTGTTCGTGTCTTTCATGATCTGGCAAGCCTGGGAGCAGGATAAAAACCCGCAACCTCAGGCCCAACAGACCACGCAGACAACGACCACCGCAGCGGGTAGCGCCGCCGACCAGGGCGTACCGGCCAGTg              <  2:173914/251‑1 (MQ=255)                                                                                                                                                                                                                                          aaaTGCCACCTTTTACACCCTGGTGGTGACGATCCCGTCCCGCCCGGACCATTTGATACCAGAGAACACTAACGATGGATTCGCAACGCAATCTTTTAGTCATCGCTTTGCTGTTCGTGTCTTTCATGATCTGGCAAGCCTGGGAGCAGGATAAAAACCCGCAACCTCAGGCCCAACAGACCACGCAGACAACGACCACCGCAGCGGGTAGCGCCGCCGACCAGGGCGTACCGGCCAGTGGCCAGGGGaa    >  1:57800/1‑250 (MQ=255)                                                                                                                                                                                                                                           aaTGCCACCTTTTACACCCTGGTGGTGACGATCCCGTCCCGCCCGGACCATTTGATACCAGAGAACACTAACGATGGATTCGCAACGCAATCTTTTAGTCATCGCTTTGCTGTTCGTGTCTTTCATGATCTGGCAAGCCTGGGAGCAGGATAAAAACCCGCAACCTCAGGCCCAACAGACCACGCAGACAACGACCACCGCAGCGGGTAGCGCCGCCGACCAGGGCGTACCGGCCAGTGGCCAGGGGAAAc  >  2:169166/1‑251 (MQ=255)                                                                                                                                                                                                                                                    |                                                                                                                                                                                                                                                  GTTGCCGACCTCGATAACCGTGCTCTCTCGGAAGCGTTGGAAAAATTATGGCGCCGCCACTGTCGCCTGGCTCGCGGGTCCTGATAGCCCTCATTCGGGTCTATCAACGCCTGATTAGTCCGCTACTCGGGCCGCATTGTCGTTTCACTCCAACCTGTTCAAGCTACGGAATTGAGGCATTGCGCAGGTTTGGAGTGATAAAAGGCAGTTGGTTGACGGTGAAACGCGTATTAAAATGCCACCCTTTACACCCTGGTGGTGACGATCCCGTCCCGCCCGGACCATTTGATACCAGAGAACACTAACGATGGATTCGCAACGCAATCTTTTAGTCATCGCTTTGCTGTTCGTGTCTTTCATGATCTGGCAAGCCTGGGAGCAGGATAAAAACCCGCAACCTCAGGCCCAACAGACCACGCAGACAACGACCACCGCAGCGGGTAGCGCCGCCGACCAGGGCGTACCGGCCAGTGGCCAGGGGAAAC  >  NC_000913/3884769‑3885253

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑