Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,457,378	C→T	L334L (CTC→CTT)	gspD →	Type II secretion system protein GspD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,457,378	0	C	T	95.0%	58.0 / ‑3.9	20	L334L (CTC→CTT)	gspD	Type II secretion system protein GspD
Reads supporting (aligned to +/- strand):  ref base C (0/1);  new base T (14/5);  total (14/6)
Fisher's exact test for biased strand distribution p-value = 3.00e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.19e-01

AGCCTTGATGTCGAAGAGAGCGAGGAAGGAAATACCCGGGTTTATTACCTGAAATATGCTAAAGCCACGAATCTGGTGGAAGTGCTAACCGGTGTTTCCGAAAAGCTGAAAGATGAAAAAGGGAATGCGCGTAAGCCCTCC‑TCTTCTGGCGCG‑ATGGATAACGTCGCCATTACCGCCGATGAACAGACTAACTCTCTGGTCATTACCGCTGACCAGTCCGTCCAGGAAAAACTCGCCACGGTAATTGCGCGTCTGGACATTCGCCGTGCACAGGTGCTGGTTGAGGCAATCATCGTTGAAGTTCAGGATGGAAATGGACTAAACCTCGGCGTGCAATGGGCGAATAAAAACGTTGGCGCACAGCAATTTACCAATACCGGATTACCGATTTTTAACGCTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCGCCTACAA  >  NC_000913/3457145‑3457623                                                                                                                                                                                                                                            |                                                                                                                                                                                                                                                      aGCCTTGATGTCGAAGAGAGCGAGCAAGGAAATACCCGGGATTATTACCTGAAATATGCTAAAGCCACGAATCTGGTGGATGTGCTAACCGGTGTTTCCGAAAAGCTGAAAGATGAAAAAGGGAATGCGCGTAAGCCCTCC‑TCTTCTGGCGCG‑ATGGATAACGTCGCCATTACCGCCGATGAACAGACTAACTCCCTGGTCATTACCTCTGACCAGTCCGTCCAGGAAAAACTTGACCCGGTAATTGcgcg                                                                                                                                                                                                                                      >  2:331938/1‑251 (MQ=255)             gAAGAGAGCGAGGAAGGAAATACCCGGGTTTATTACCTGAAATATGCTAAAGCCACGAATCTGGTGGAAGTGCTAACCGGTGTTTCCGAAAAGCTGAAAGATGAAAAAGGGAATGCGCGTAAGCCCTCC‑TCTTCTGGCGCG‑ATGGATAACGTCGCCATTACCGCCGATGAACAGACTAACTCTCTGGTCATTACCGCTGACCAGTCCGTCCAGGAAAAACTTGCCACGGTAATTGCGCGTCTGGACATTCg                                                                                                                                                                                                                          >  1:188595/1‑251 (MQ=255)               agagagCGAGGAAGGAAATACCCGGGTTTATTACCTGAAATATGCTAAAGCCACGAATCTGGTGGAAGTGCTAACCGGTGTTTCCGCAAAGCTGAAAGATGAAAAAGGGAATGCGCGTAAGCCCTCC‑TCTTCTGGCGCG‑ATGGATAACGTCGCCATTACCGCCGATGAACAGACTAACTCTCTGGTCATTACCGCTGACCAGTCCGTCCAGGAAAAACTTGCCACGGTAATTGCGCGTCTGGACATTCGcc                                                                                                                                                                                                                        >  1:319728/1‑251 (MQ=255)                        ggaaggaaATACCCGGGTTTATTACCTGAAATATGCTAAAGCCACGAATCTGGTGGAAGTGCTAACCGGTGTTTCCGAAAAGCTGAAAGATGAAAAAGGGAATGCGCGTAAGCCCTCC‑TCTTCTGGCGCG‑ATGGATAACGTCGCCATTACCGCCGATGAACAGACTAACTCTCTGGTCATTACCGCTGACCAGTCCGTCCAGGAAAAACTTGCCACGGTAATTGCGCGTCTGGACATTCGCCGTGCACAgg                                                                                                                                                                                                               >  1:133306/1‑251 (MQ=255)                                                ccTGAAATATGCTAAAGCCACGAATCTGGTGGAAGTGCTAACCGGTGTTTCCGAAAAGCTGAAAGATGAAAAAGGGAATGCGCGTAAGCCCTCC‑TCTTCTGGCGCG‑ATGGATAACGTCGCCATTACCGCCGATGAACAGCCTAACTCTCTGGTCATTACCGCTGACCAGTCCGTCCAGGAAAAACTTGCCACGGTAATTGCGCGTCTGGACATTCGCCGTGCACCGGTGCTGGTTGAGGCAATCATCGTTg                                                                                                                                                                                       >  2:29358/1‑251 (MQ=255)                                                               aGCCACGAATCTGGTGGAAGTGCTAACCGGTGTTTCCGAAAAGCTGAAAGATGAAAAAGGGAATGCGCGTAAGCCCTCC‑TCTTCTGGCGCG‑ATGGATAACGTCGCCATTACCGCCGATGAACAGACTAACTCTCTGGTCATTACCGCTGACAAGTCCGGCCAGGAAAAACTTGCCACGGTAATTGCGTGTCTGGACTTTCGCCGAGCACAGGTCCTGGGTGGGGAAATCATCGTTGTAGTTCAGTATGGa                                                                                                                                                                         >  2:282928/1‑250 (MQ=255)                                                                 ccACGAATCTGGTGGAAGTGCTAACCGGTGTTTCCGAAAAGCTGAAAGATGAAAAAGGGAATGCGCGTAAGCCCTCC‑TCTTCTGGCGCG‑ATGGATAACGTCGCCATTACCGCCGATGAACAGACTAACTCTCTGGTCATTACCGCTGACCAGTCCGTCCAGGAAAAACTTGCCACGGTAATTGCGCGTCTGGACATTCGCCGTGCACAGGTGCTGGTTGAGGCAATCATCGTTGAAGTTCAGGATGGAAAt                                                                                                                                                                      >  1:81440/1‑251 (MQ=255)                                                                                               tttCCGAAAAGCTGAAAGCTGAAAAAGGGAATGCGCGGAAGCCCTCC‑TCTTCTGGCGCG‑ATGGATAACGTCGCCATTACCGCCGATGAACAGACTAACTCTCTGGTCATTACCGCTGACCAGTCCGTCCAGGAAAAACTTGCCCCGGAAATTGCGCGTCTGGACATTCGCCGTGCACCGGTGCTGGTTGAGGCAATCCTCGTTGAAGTTCAGGTTGGAAATGGCATAAACAGCGGAGTGGCATGGGCGAAt                                                                                                                                        >  2:50426/1‑251 (MQ=255)                                                                                                   cGAAAAGCTGAAAGATGAAAAAGGGAATGCGCGTAAGCCCTCC‑TCTTCTGGCGCG‑ATGGATAACGTCGCCATTACCGCCGATGAACAGACTAACTCTCTGGTCATTACCGCTGACCAGTCCGTCCAGGAAAAACTTGCCa                                                                                                                                                                                                                                                   >  1:292781/1‑140 (MQ=255)                                                                                                            aaaaaaaaaaaacGGGAATGCGAG‑AACCCCTCCCTCTTGGGGCGCG‑ATGGTCAACGTCTCCAGTCCCGCCGATGAACAGACTAACTCTCTGGTCATTACCGCTGACCAGTCCGTCCAGGAAAAACTCGCCACGGTAATTGCGCGTCTGGACATTCGCCGTGCACAGGTGCTGGTTGAGGCAATCATCGTTGAAGTTCAGGATGGAAATGGACTAAACCTCGGCGTGCAATGGGCGAATAAAAACGTTGgcg                                                                                                                           <  2:166469/243‑1 (MQ=255)                                                                                                                       aaGGGAATGCGCTTACCCCCTCC‑TCTTC‑GGCGGGGATGGATACCGCCGCCATTACCGCCGATGAACAGACTAACTCTCTGGTCATTACCGCTGACCAGTCCGTCCAGGAAAAACTTGCCACGGTAATTGCGCGTCTGGACATTCGCCGTGCACAGGTGCTGGTTGAGGCAATCATCGTTGAAGTTCAGGATGGAAATGGACTAAACCTCGGCGTGCAATGGGCGAATAAAAACGTTGGCGCACAGCAAttt                                                                                                                <  1:43063/251‑1 (MQ=255)                                                                                                                                            ccctctgcgggggcg‑AGGGATACCGTCGCCATTACCGCCGATGAACAGACTAACTCTCTGGTCATTACCGCTGACCAGTCCGTCCAGGAAAAACTTGCCACGGTAATTGCGCGTCTGGACATTCGCCGTGCACAGGTGCTGGTTGAGGCAATCATCGTTGAAGTTCAGGATGGAAATGGACTAAACCTCGGCGTGCAATGGGCGAATAAAAACGTTGGCGCACAGCAATTTACCAATACCGGATTACCGAt                                                                                            <  1:29358/239‑1 (MQ=255)                                                                                                                                                                                                aaCTCTCTGGTCATTACCGCTGACCAGTCCGTCCAGGAAAAACTTGCCACGGTAATTGCGCGTCTGGACATTCGCCGTGCACAGGTGCTGGTTGAGGCAATCATCGTTGAAGTTCAGGATGGAAATGGACTAAACCTCGGCGTGCAATGGGCGAATAAAAACGTTGGCGCACAGCAATTTACCAATACCGGATTACCGATTTTTAACGCTGCGCAAGGAGGGGCTGATTATAAAAAGAATGGTGGGCTCAc                                         >  2:31059/1‑251 (MQ=255)                                                                                                                                                                                                           catgaCCGCTGACCAGTCCGTCCAGGAAAACCTTGCCACGGTAATTGCGCGTCTTGACATTCGCCGTGCACAGGTGCTGGTTGAGGCAATCATCGTTGAAGTTAAGGATGGAAATGGACTAAACCTCAGCGTGCAGTGGGCGAATAAAAACGTTGGCGCACAGCAATTTACCAATACCGGATTACCGATTTTTAACGCTGCGCAAGGTGTGGCTGATTATAACAAGACTGGGTGGATCACCAGCGCGatgc                              >  2:53144/5‑248 (MQ=255)                                                                                                                                                                                                                         aGTCCGTCCAGGAAAAACTTGCCACGGTAATTGCGCGTCTGGACATTCGCCGTGCACAGGTGCTGGTTGAGGCAATCATCGTTGAAGTTCAGGATGGAAATGGACTAAACCTCGGCGTGCAATGGGCGAATAAAAACGTTGGCGCACAGCAATTTACCAATACCGGATTACCGATTTTTAACGCTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCa                                          <  1:60948/225‑1 (MQ=255)                                                                                                                                                                                                                         aGTCCGTCCAGGAAAAACTTGCCACGGTAATTGCGCGTCTGGACATTCGCCGTGCACAGGTGCTGGTTGAGGCAATCATCGTTGAAGTTAAGGATGGAAATGGACTAAACCTCGGCGTGCAATGGGCGAATAAAAACGTTGGCGCACAGCAATTTACCAATACCGGATTACCGATTTTTAACGCTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCaagataggaagagcgtcgggtagggc                 >  2:60948/1‑225 (MQ=255)                                                                                                                                                                                                                           gacggcccggAAAAACTTGCCACGGTAATTGAGCGTCTGGAAATTCGTCGTGCACAGGTGCTGGTTGAGGCAATCATCGTTGAAGTTCAGGATGGAAATGGACTAATCCTCGGCGTGCAATGGGCGAATAAAAACGTTGGCGCACAGCAATTTACCAATTCCGGATTACCGATTTTTAACGCTGCGCAAGGTGTGGCCGATTATAAAAAGAATGGTGGGATCTCCAGCGCGAATCCTGCCTGGGATATGtt              <  2:188595/243‑1 (MQ=255)                                                                                                                                                                                                                                      aaaaCTTGCCACGGTAATTGCGCGTCTGGACATTCGCCGTGCACAGGTGCTGGTTGAGGCAATCATCGTTGAAGTTCAGGATGGAAATGGACTAAACCTCGGCGTGCAATGGGCGAATAAAAACGTTGGCGCACAGCAATTTACCAATACCGGATTACCGATTTTTAACGCTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTgg                      <  2:23016/232‑1 (MQ=255)                                                                                                                                                                                                                                      aaaaCTTGCCACGGTAATTGCGCGTCTGGACATTCGCCGTGCACAGGTGCTGGTTGAGGCAATCATCGTTGAAGTTCAGGATGGAAATGGACTAAACCTCGGCGTGCAATGGGCGAATAAAAACGTTGGCGCACAGCAATTTACCAATACCGGATTACCGATTTTTAACGCTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTgg                      >  1:23016/1‑232 (MQ=255)                                                                                                                                                                                                                                        aaCTTGCCACGGTAATTGCGCGTCTGGACATTCGCCGTGCACAGGTGCTGGTTGAGGCAATCATCGTTGAAGTTCAGGATGGAAATGGACTAAACCTCGGCGTGCAATGGGCGAATAAAAACGTTGGCGCACAGCAATTTACCAATACCGGATTACCGATTTTTAACGCTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGCTATGTTTAGCGCCTACaa  >  1:112488/1‑250 (MQ=255)                                                                                                                                                                                                                                            |                                                                                                                                                                                                                                                      AGCCTTGATGTCGAAGAGAGCGAGGAAGGAAATACCCGGGTTTATTACCTGAAATATGCTAAAGCCACGAATCTGGTGGAAGTGCTAACCGGTGTTTCCGAAAAGCTGAAAGATGAAAAAGGGAATGCGCGTAAGCCCTCC‑TCTTCTGGCGCG‑ATGGATAACGTCGCCATTACCGCCGATGAACAGACTAACTCTCTGGTCATTACCGCTGACCAGTCCGTCCAGGAAAAACTCGCCACGGTAATTGCGCGTCTGGACATTCGCCGTGCACAGGTGCTGGTTGAGGCAATCATCGTTGAAGTTCAGGATGGAAATGGACTAAACCTCGGCGTGCAATGGGCGAATAAAAACGTTGGCGCACAGCAATTTACCAATACCGGATTACCGATTTTTAACGCTGCGCAAGGTGTGGCTGATTATAAAAAGAATGGTGGGATCACCAGCGCGAATCCTGCCTGGGATATGTTTAGCGCCTACAA  >  NC_000913/3457145‑3457623

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑