Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,652,331	T→C	intergenic (+2346/+397)	ydfD → / ← ynfP	lysis protein/protein YnfP

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,652,331	0	T	C	96.7%	103.7 / NA	31	intergenic (+2346/+397)	ydfD/ynfP	lysis protein/protein YnfP
Reads supporting (aligned to +/- strand):  ref base T (0/1);  new base C (16/13);  total (17/14)
Fisher's exact test for biased strand distribution p-value = 4.67e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.91e-01

ATGGTGTGTTTCTGTTTATACTGGAGTTCGCCCTGGTGAGCTGTGTGCACTTGGATGGGAGGACATAGATCTGAAAAATGGAACAATGATGATCAGGAGAAATTTAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGTCATTCATCTTATTAAGCCAGCAATCGACGCTCTCCGGAGTCAGATGACATTAACGAGACTGAGCAAAGAGCATATCATTGATGTTCACTTCAGAGAGTATGGC‑AGAACAGAAAAACAAAAATGCACCTTT‑GTTTTTCAACCTGAAGTGTCAGCGAGAGTAAAAAATTATGGTGACCATTTTACCGTTGACTCAATAAGGCAGATGTGGGACGCAGCGATAAAACGTGCCGGACTCCGCCATCGAAAATCATATCAGTCGAGACATACTTATGCCTGCTGGTCGCTGACAGCTGGTGCTAACCCGGCATTTATAGCAAACCAGATGGGCCATGC  >  NC_000913/1652087‑1652575                                                                                                                                                                                                                                                     |                                                                                                                                                                                                                                                       aTGGAGTGTTTCTGTTTATACTGGAGTTCGCCCTGGTGAGCTGTGTGCACTTGGATGGGAGGACATAGATCTGAAAAATGGAACAATGATGATCAGGAGAAATTTAGCAACAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAAACGGGGCCTTCATCTTATTTAGACAGCCATCGCCGCCATCCCGAGTCAGATGAAATTAACGAGACTGCGNAAAGAACATATCATTGATGTTAACCTCaga                                                                                                                                                                                                                                                   >  2:234829/1‑250 (MQ=255)           tCTGTTTATACTGGAGTTCGCCCTGGTGAGCTGTGTGCACTTGGATGGGAGGACATAGATCTGAAAAATGGAACAATGATGATCAGGAGAAATTTAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGGCATTCATCTTATTAAGCCAGCAATCGACGCTCTCCGGAGGCAGATGACATTAACGGGACTGAGCAAAGAGCAAATCATTGATGTTCACCTCAGAGAGGATGGc                                                                                                                                                                                                                                          >  1:151866/1‑249 (MQ=255)              gTTTATACTGGAGTTCGCCCTGGTGAGCTGTGTGCACTTGGATGGGAGGACATAGATCTGAAAAATGGAACAATGATGATCAGGAGAAATTTAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGTCATTCATCTTATTAAGCCAGCAATCGACGCTCTCCGGAGTCAGATGACATTAACGAGACTGAGCAAAGAGCATATCATTGATGTTCACCTCAGAGAGTATGGc‑agaac                                                                                                                                                                                                                                    <  1:192656/251‑1 (MQ=255)                        gAGTTCGCCCTGGTGAGCTGTGTGCACTTGGATGGGAGGACATAGATCTGAAAAATGGAACAATGCTGATCAGGAGAAATTTAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGGACCCAAAAGGTCCTTCATCTTATTAAACACGCCATCGACGCCATCAGGAGTCAGATGATATATACAAGACAGTGCAAAGAGCATATCATTGATGTTAACCTCAGAGAGGATGGt‑agaacaacaaaaaa                                                                                                                                                                                                                           >  2:409418/1‑242 (MQ=255)                                    gTGAGCTGTGTGCACGTGGATGGGAGGACATAGATCTGAAAAATGGAACAATGATGATCAGGAGAAATTTAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGTCATTCATCTTATTAAGCCAGCAATCGACGCTCTCCGGAGTCAGAGGACATTAACGAGACTGAGCAAAGAGCATATCATTGATGTTCACTTGAGATAGTATGTC‑AGAACAGAAAAACAAAAATGCTCCttt                                                                                                                                                                                                              <  2:270118/251‑1 (MQ=255)                                               gCACTTGGATGGGAGGACATAGATCTGAAAAATGGAACAATGATGATCAGGAGAAATTTAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGTCATTCATCTTATTAAGCCAGCAATCGACGCTCTCCGGAGTCAGATGACATTAACGAGACTGAGCAAAGAGCATATCATTGATGTTCACCTCTGAGAGTATGGC‑AGAACAGAAAAACAAAAATGCACCTTT‑GTTTTTCAAcc                                                                                                                                                                                                  <  1:248321/251‑1 (MQ=255)                                                    tGGATGGGAGGACATAGATCTGAAAAATGGAACAATGATGATCAGGAGAAATTTAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAAACGGGTAAATCATCTTATTAAACCAGAAATAGACGCCCTCCGGGGTCAAATGAAATTAAAGCGACTGAGCAAAGAGCAAATCAATGATGTTCACATCAAAGAGGATGGC‑AGAAAAGAAAAAAAAAAAAGCACCTTT‑GTTTTTTAACCTGa                                                                                                                                                                                               >  1:121272/1‑249 (MQ=255)                                                         gggAGGACATAGATCTGAAAAATGGAACAATGATGATCAGGAGAAATTTAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGTCATTCATCTTATTAAGCCAGCAATCGACGCTCTCCGGAGTCAGATGACATTAACGAGACTGAGCAAAGAGCATATCATTGATGTTCACCTCAGAGAGTATGGC‑AGAACAGAAAAACAAAAATGCACCTTT‑GTTTTTCAACCTGAAGTGTc                                                                                                                                                                                         <  1:336296/250‑1 (MQ=255)                                                           gaggaCATAGATCTGAAAAATGGAACAATGATGATCAGGAGAAATTTAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAAACAATCAGGGCATTCATCTTTTTAAACCAGCAATCGACGCTCTCCGGGGTCAGATGACATTAACGAGCCTGGGCAAAGAGCATATCATTGATGTTTACCTCAGAGAGTATGGC‑AGAACAAAAAAAAAAAAATGCACCTTT‑GTTTTTCAACCTGAAATGTCaac                                                                                                                                                                                      >  1:33203/1‑249 (MQ=255)                                                            aggaCATAGATCTGAAAAATGGAACAATGATGATCAGGAGAAATTTAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGTCATTCATCTTATTAAGCCAGCAATCGACGCTCTCCGGAGTCAGATGACATTAACGAGACTGAGCAAAGAGCATATCATTGATGTTCACCTCAGAGAGTATGGC‑AGAACAGAAAAACAAAAATGCACCTTT‑GTTTTTCAACCTGAAGTGTCAGCg                                                                                                                                                                                     <  2:151866/251‑1 (MQ=255)                                                                       cTGAAAAATGGAACAATGATGATCAGGAGAAATTTAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGGCAATCATCTTATTAAGCCAGCAATCGACGCTCTCCCGAGTCAGATGACATTAAAGAGGATGAGCAAAAAGCATATCATTGATGTTCACCTCCGAGAGGAAGGC‑AGGACAAAAAAAAAAAAAAGCACCTTTTGTTTTT‑AACCTGAAGTGTCAGCGCGAGGaaaaa                                                                                                                                                                           >  1:37980/1‑250 (MQ=255)                                                                        tGAAAAATGGAACAATGATGATCAGGAGAAATTTAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAAACGGGTCATTCATCTTATTAAGCCAGCAATCGACGCTCTCCGGCGTCAGATGACATTAACGAGACTGAGCAAAGAGCATATCATTGATGTTTACCTCAGAGAGTATGGC‑AGAACAGAAAAACAAAAATGCACCTTT‑GTTTTTCAACCTGAAGTGTCATCGGGAGGaaaaaa                                                                                                                                                                          >  2:47661/1‑250 (MQ=255)                                                                         gAAAAATGGAACAATGATGATCAGGAGAAAGTTAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGTCATTCATCTTATTAAGCCAGCAATCGACGCTCTCCGGAGTCAGATGACATTAACGAGACTGAGCAAAGAGCATATCATTGATGTTCACCTCAGAGATTATGGC‑AGAACTGAAAAGCAAAAATGCGCCTTT‑GTTTTTCAACCTGAAGTGTCAGCGAGAGTAAAAAAt                                                                                                                                                                         <  1:394865/250‑1 (MQ=255)                                                                          aaaaaTTGAACAATGATGATCATGAGAAATTTAGCAAAAGACCATGTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGTCATTCATCTTATTACGCCAGCAATCGACGCTCTCCGGAGTCAGATGACATTAACGATACTGAGCAAAGAGCATATCATTTATGTTCACCTCAGATAGTATGGC‑AGAACAGAAAAACAAAAATGCACCTTT‑GTTTTTCAACCTGAAGTGTCAGCGAGAGTAAAAATTTa                                                                                                                                                                       <  2:275411/251‑1 (MQ=255)                                                                           aaaaTGGAACAATGATGATCAGGAGAAATTTAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGTCATTCATCTTATTAAGCCAGCAATCGACGCTCTCCGGAGTCAGATGACATTAACGAGACTGAGCAAAGAGCATATCATTGATGTTCACCTCAGAGAGTATGGC‑AGAACAGAAAAACAAAAATGCACCTTT‑GTTTTTCAACCTGAAGTGTCAGCGAGAGTAAAAAATTAt                                                                                                                                                                      <  1:160059/251‑1 (MQ=255)                                                                             aaTGGAACAATGATGATCAGGAGAAATTTAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAAACAAACGGGGCATTCCTCTTATTAAACCAACCAACGACGCCCTCCGGAGGCAGCTGACATTAACAAGACTTAGCAAAGAGCAAATCATTTTTGTTCACCTCAAAAAGTATGGCCACAA‑AAAAAAACAAAAATGCACCTTT‑GTTTTTTACCCTGACGTGTCCCCGAGAGCAAAAAAATATgg                                                                                                                                                                    >  2:325090/1‑251 (MQ=255)                                                                                           gatCAGGAGAAATTTAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGTCATTCATCTTATTAAGCCAGCAATCGACGCTCTCCGGAGTCAGATGACATTAACGAGACTGAGCAAAGAGCATAACATTGATGTTCACCTCAGAGAGTATGGC‑AGAACAGAAAATCAAAAATGCACCTTT‑GTTTTTCAACCTGAAGTGTCAGCGAGAGTAAAAAATTATGGTGACCATTTTAcc                                                                                                                                                       <  2:301637/250‑1 (MQ=255)                                                                                                 gagaAATTTAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGTCATTCATCTTATTAAGCCAGCAATCGACGCTCTCCGGAGTCAGATGACATTAACGAGGCTGAGCAAAGAGCATATCATTGATGTTCACCTCAGAGAGTATGGC‑AGAACAGAAAAACAAAAATGCACCTTT‑GTTTTTCAACCTGAAGTGTCAGCGAGAGTAAAAAATTATGGGGACCATTTTACCGTTGACt                                                                                                                                                >  1:125921/1‑251 (MQ=255)                                                                                                              aaaGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGTCATTCATCTTATTAAGCCAGCAATCGACGCTCTCCGGAGTCAGATGACATTAACGAGACTGAGCAAAGAGCATATCATTGATGTTCACCTCAGAGAGTATGGC‑AGAACAGAAAAACAAAAATGCACCTTT‑GTTTTTCAACCTGAAGTGTCAGCGAGAGTAAAAAATTATGGTGACCATTTTACCGTTGACTCAATAAGGCAGAt                                                                                                                                   <  1:60144/251‑1 (MQ=255)                                                                                                                                        acaGGCGGGAACCAATCGGGTCATTCATCTTATTAAGCCAGCAATCGACGCTCTCCGGAGTCAGATGACATTAACGAGACTGAGCAAAGAGCATATCATTGATGTTCACCTCAGAGAGTATGGC‑AGAACAGAAAAACAAAAATGCACCTTT‑GTTTTTCAACCTGAAGTGTCAGCGAGAGTAAAAAATTATGGTGACCATTTTACCGTTGACTCAATAAGGCAGATGTGGGACGCAGCGATAAAACGTGCCg                                                                                                         <  2:265496/251‑1 (MQ=255)                                                                                                                                              gggAATCAATCGGGTCATTTATCATATTAAGCCAGCAATTGACGCTCTCCGTAGTCAGATGAAATTAACGTTACTGAACAAAGAGCATATCATTGATGTTCACCTCAGAGAGTATGGC‑AGAACAGAAAAACAAAAATGCACCTTT‑GTTTTTCAACCCGAAGTGTCAGCGAGAGTCAAAAAGTATGGTGACCATTTTACCGTTGACGCAATAAGGCAGATGTGGGACGCTGCGATAAAACGTGCCGGACTcc                                                                                                   <  2:3573/251‑1 (MQ=255)                                                                                                                                                          gggccttcatCTTATTAAGCCAGCAATCGACGCTCTCCGGAGTCAGATGACTTTAACGAGCCTGAGCAAAGAGCATATCATTGTTGCTAACCTCAGAGAGTATGAC‑AGCACAGAAAAACAAAAATGCACCTTT‑GTTTTTCACCCTGAAGAGTCAGCGAGAGTAAAAACTTATGGTGACCATTTTACCGTTGACTCAATAAGGCAGATGTGGGACGCAGCGATAAAACGGGCCGGACTCCGCCATCGaacat                                                                                       >  2:6517/6‑248 (MQ=255)                                                                                                                                                                      tattaAGCCAGCAATCGACGCTCTCCGGAGTCAGATGACATTAACGAGACTGAGCAAAGAGCATATCATTGATGTTCACCTCAGAGAGTATGGC‑AGAACAGAAAAACAAAAATGCACCTTT‑GTTTTTCAACCTGAAGTGTCAGCGAGAGTAAAAAATTATGGTGACCATTTTACCGTTGACTCAATAAGGCAGATGTGGGACGCAGCGATAAAACGTGCCGGACTCCGCCATCGAAAATCATATCAGTCg                                                                            >  1:360947/1‑250 (MQ=255)                                                                                                                                                                                              ccGGAGTCAGATGACATTAACGAGACTGAGCAAAGAGCATATCATTGATGTTCACCTCAGAGAGTATGGC‑AGAACAGAAAAACAAAAATGCACCTTT‑GTTTTTCAACCTGAAGTGTCAGCGAGAGTAAAAAATTATGGTGACCATTTTACCGTTGACTCAATAAGGCAGATGTGGGACGCAGCGATAAAACGTGCCGGACTCCGCCATCGAAAATCATATCAGTCGAGACATACTTATGCCTGCTGGTCGc                                                   >  2:264206/1‑251 (MQ=255)                                                                                                                                                                                                          gACATTAACGAGACTGAGCAAAGAGCATATCATTGATGTTCACCTCAGAGAGTATGGC‑AGAACAGAAAAACAAAAATGCACCTTT‑GTTTTTCAACCTGAAGTGTCAGCGAGAGTAAAAAATTATGGTGACCATTTTACCGTTGACTCAATAAGGCAGATGTGGGACGCAGCGATAAAACGTGCCGGACTCCGCCATCGAAAATCATATCAGTCGAGACATACTTATGCCTGCTGGTCGCTGACAGCTGGt                                        <  1:107937/250‑1 (MQ=255)                                                                                                                                                                                                                    agaCTGAGCAAAGAGCATATCATTGATGTTCACCTCAGAGAGTATGGC‑AGAACAGAAAAACAAAAATGCACCTTT‑GTTTTTCAACCTGAAGTGTCAGCGAGAGTAAAAAATTATGGTGACCATTTTACCGTTGACTCAATAAGGCAGATGTGGGACGCAGCGATAAAACGTGCCGGACTCCGCCATCGAAAATCATATCAGTCGAGACATACTTATGCCTGCTGGTCGCTGACAGCTGGTGCTAACCCGGc                             >  1:231779/1‑251 (MQ=255)                                                                                                                                                                                                                         gAGCAAAGAGCATATCATTGATGTTCACCTCAGAGAGTATGGC‑AGAACAGAAAAACAAAAATGCACCTTT‑GTTTTTCAACCTGAAGTGTCAGCGAGAGTAAAAAATTATGGTGACCATTTTACCGTTGACTCAATAAGGCAGATGTGGGACGCAGCGATAAAACGTGCCGGACTCCGCCATCGAAAATCATATCAGTCGAGACATACTTATGCCTGCTGGTCGCTGACAGCTGGTGCTAACCCGGCAttt                         <  1:22595/250‑1 (MQ=255)                                                                                                                                                                                                                         gAGCAAAGAGCATATCATTGATGTTCACCTCAGAGAGTATGGC‑AGAACAGAAAAACAAAAATGCACCTTT‑GTTTTTCAACCTGAAGTGTCAGCGAGAGTAAAAAATTATGGTGACCATTTTACCGTTGACTCAATAAGGCAGATGTGGGACGCAGCGATAAAACGTGCCGGACTCCGCCATCGAAAATCATATCAGTCGAGACATACTTATGCCTGCTGGTCGCTGACAGCTGGTGCTAACCCGGCAttt                         >  2:169336/1‑250 (MQ=255)                                                                                                                                                                                                                              aaGAGCATATCATTGATGTTCACCTCAGAGAGTATGGC‑AGAACAGAAAAACAAAAATGCACCTTT‑GTTTTTCAACCTGAAGTGTCAGCGAGAGTAAAAAATTATGGTGACCATTTTACCGTTGACTCAATAAGGCAGATGTGGGACGCAGCGATAAAACGTGCCGGACTCCGCCATCGAAAATCATATCAGTCGAGACATACTTATGCCTGCTGGTCGCTGACAGCTGGTGCTAACCCGGCATTTATAGc                    >  1:208417/1‑250 (MQ=255)                                                                                                                                                                                                                                      atCATTGATGTTCACCTCAGAGAGTATGGC‑AGAACAGAAAAACAAAAATGCACCTTT‑GTTTTTCAACCTGAAGTGTCAGCGAGAGTAAAAAATTATGGTGACCATTTTACCGTTGACTCAATAAGGCAGATGTGGGACGCAGCGATAAAACGTGCCGGACTCCGCCATCGAAAATCATATCAGTCGAGACATACTTATGCCTGCTGGTCGCTGACAGCTGGTGCTAACCCGGCATTTATAGCAAAcc               >  1:221017/1‑247 (MQ=255)                                                                                                                                                                                                                                                ttCACCTCAGAGAGTATGGC‑AGAACAGAAAAACAAAAATGCACCTTT‑GTTTTTCAACCTGAAGTGTCAGCGAGAGTAAAAAATTATGGTGACCATTTTACCGTTGACTCAATAAGGCAGATGTGGGACGCAGCGATAAAACGTGCCGGACTCAGCCATAGAAAATCATATCAGTCGAAACATACTTATGCCTGCTGGTAGCTGACAGCTGGTGCTAACCCGCCATTTATCGTAATCCAGATGGGCCATGc  >  2:75022/1‑250 (MQ=255)                                                                                                                                                                                                                                                     |                                                                                                                                                                                                                                                       ATGGTGTGTTTCTGTTTATACTGGAGTTCGCCCTGGTGAGCTGTGTGCACTTGGATGGGAGGACATAGATCTGAAAAATGGAACAATGATGATCAGGAGAAATTTAGCAAAAGACCGTTTCACGGTACCAAAAACACAGGCGGGAACCAATCGGGTCATTCATCTTATTAAGCCAGCAATCGACGCTCTCCGGAGTCAGATGACATTAACGAGACTGAGCAAAGAGCATATCATTGATGTTCACTTCAGAGAGTATGGC‑AGAACAGAAAAACAAAAATGCACCTTT‑GTTTTTCAACCTGAAGTGTCAGCGAGAGTAAAAAATTATGGTGACCATTTTACCGTTGACTCAATAAGGCAGATGTGGGACGCAGCGATAAAACGTGCCGGACTCCGCCATCGAAAATCATATCAGTCGAGACATACTTATGCCTGCTGGTCGCTGACAGCTGGTGCTAACCCGGCATTTATAGCAAACCAGATGGGCCATGC  >  NC_000913/1652087‑1652575

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑