Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	266,358	0	T	G	51.7%	28.0 / 45.4	29	T66P (ACC→CCC)	yafY	lipoprotein, inner membrane; degP regulator; CP4‑6 prophage
Reads supporting (aligned to +/- strand):  ref base T (3/11);  new base G (15/0);  total (18/11)
Fisher's exact test for biased strand distribution p-value = 1.05e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.13e-05

CCTCCTGGTATTCCAGTTTGATGTTATCGGCAATACACAGCGCATTCATCAGTGGCTGGACGGTTTTTTCCTGCATATCCACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGTACGT‑AAAACCTGCAAGGTGGGACCGGATAAGTAGTCAACCTGTG‑ACCATTCTTCGCTGACATCATCCTGGTGGCTGACCACATCACTGAAACGCGGTGGGGTGAGGTCCTTAAATTTACTGATGGCCTTCAGGTCATCACTTCTGTCATCGCATGCGATGAGAAAC  >  NC_000913/266211‑266506                                                                                                                                                     |                                                                                                                                                      cctcctGGTATTCCAGTTTGATGTTATCGGCAATACACAGCGCATTCATCAGTGGCTGGACGGTTTTTTCCTGCATATCCACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGTACGT‑AAAACCTGCAAGGTggg                                                                                                                                                    <  1:578243/151‑1 (MQ=255)          aTTCCAGTTTGATGTTATCGGCAATACACAGCGCATTCATCAGTGGCTGGACGGTTTTTTCCTGCATATCCACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGGGAGT‑AAAAACCGCCAAGGGGGGCCgggga                                                                                                                                            >  1:474696/1‑147 (MQ=255)               aGTTTGATGTTATCGGCAATACACAGCGCATTCATCAGTGGCTGGACGGTTTTTTCCTGCATATCCACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGTACGT‑AAAACCTGCAAGGTGGGACCGGATAagtagt                                                                                                                                      <  1:50783/151‑1 (MQ=255)                gTTTGATGTTATCGGCAATACACAGCGCATTCATCAGTGGCTGGACGGTTTTTTCCTGCATATCCACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTAGCGGGTACGT‑AAAACCTGCAAGGGGGGACCGGATAAGTAGTc                                                                                                                                     >  1:490482/1‑151 (MQ=255)                    gATGTTATCGGCAATACACAGCGCATTCATCAGTGGCTGGACGGTTTTTTCCTGCATATCCACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGGACGG‑AAAAACTTCAAGGGGGGGCCGGGTAAAAAGTCaaac                                                                                                                                 >  2:69020/1‑149 (MQ=255)                     aTGTTATCGGCAATACACAGCGCATTCATCAGTGGCTGGACGGTTTTTTCCTGCATATCCACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGGGAGTAAAAACCTGAAAGGGGGGCCCgataaagagtgcaac                                                                                                                                  >  1:520627/1‑136 (MQ=255)                             ggCAATACACAGCGCATTCATCAGTGGCTGGACGGTTTTTTCCTGCATATCCACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGTACGT‑AAAACCTGCAAGGTGGGACCGGATAAGTAGTCAACCTGTG‑ACCAt                                                                                                                       <  2:463907/151‑1 (MQ=255)                              gCAATACACAGCGCATTCATCAGTGGCTGGACGGTTTTTTCCTGCATATCCACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGGAAGT‑AAAAACTGCAAGGGGGGGCCGGATAAAGAGTCAACCTGTG‑ACCCtt                                                                                                                      >  2:517453/1‑151 (MQ=255)                               cAATACACAGCGCATTCATCAGTGGCTGGACGGTTTTTTCCTGCATATCCACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGTAAGT‑AAAAACCGCAAGGGGGGGCCGGATAAATAGTCAACCTGTG‑ACCAtt                                                                                                                      >  2:392657/1‑150 (MQ=255)                                 aTACACAGCGCATTCATCAGTGGCTGGACGGTTTTTTCCTGCATATCCACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGTACGT‑AAAACCTGCAAGGTGGGACCGGATAAGTAGTCAACCTGTG‑ACCAttctt                                                                                                                   <  2:184034/151‑1 (MQ=255)                                  tACACAGCGCATTCATCAGTGGCTGGACGGTTTTTTCCTGCATATCCACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGGGAGT‑GAAAAACGCAAGGGGGGGCCCGGTAAGGAGGCAACCcgttgccactttt                                                                                                                    >  1:86034/1‑140 (MQ=255)                                     acaGCGCATTCATCAGTGGCTGGACGGTTTTTTCCTGCATATCCACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGTACGT‑AAAACCTGCAAGGTGGGACCGGATAAGTAGTCAACCTGTG‑ACCATTCTTCGCt                                                                                                               <  2:271491/151‑1 (MQ=255)                                     acaGCGCATTCATCAGTGGCTGGACGGTTTTTTCCTGCATATCCACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGTACCT‑CAAACCCGCAAGGGGGGGCCGGGTAAGTAGTCAACCTGTG‑GCCAttctt                                                                                                                   >  1:248325/1‑147 (MQ=255)                                       aGCGCATTCATCAGTGGCTGGACGGTTTTTTCCTGCATATCCACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGGACGT‑AAAAACTGCAAGGGGGGGCCGGGTAAATAAGCAACCTGTG‑TCCAttctt                                                                                                                   >  2:66511/1‑145 (MQ=255)                                             ttCATCAGTGGCTGGACGGTTTTTTCCTGCATATCCACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGGACGT‑AAAAACCGCAAAGGGGGAACGGATAAAGAGGCAACCTGTG‑ACCATTTTTTTCTGAca                                                                                                           >  2:102874/1‑147 (MQ=255)                                                  caGTGGCTGGACGGTTTTTTCCTGCATATCCACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGTACGT‑AAAACCTGCAAGGTGGGACCGGATAAGTAGTCAACCTGTG‑ACCATTCTTCGCTGACATCATCCtg                                                                                                   <  1:577757/150‑1 (MQ=255)                                                     tGGCTGGACGGTTTTTTCCTGCATATCCACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGTACGT‑AAAAACCGCAAGGTGGGGCGCGATAAATAATCAACCTGTG‑AACATTCTTCCCTGACATCATCCtggtg                                                                                                >  2:10762/1‑150 (MQ=255)                                                      ggCTGGACGGTTTTTTCCTGCATATCCACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGGAGGT‑AAAACCTGGAAGGGGGGCCCGGGGAAGGAAGCAACCTGGG‑ACCATTCTTTGCTGACACCAACCtggtgg                                                                                               >  1:370280/1‑150 (MQ=255)                                                                       cTGCATATCCACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGGACGG‑AAAAACTGCAAGGGGGGGCCGGATAAATAGGCAAACTGTG‑ACCATTCTTCTCTTACATCATCCTGGGGGGTGAACCCAacacctaa                                                                              >  2:31092/1‑146 (MQ=255)                                                                        tGCATATCCACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGTACGT‑AAAACCTGCCAGGTGGGACCGGGTAAGTAGTCAACCTGTG‑ACCATTCTTCGCTGACATCATCCTGGGGGCTGACCACATCACTGaaa                                                                             >  2:286798/1‑150 (MQ=255)                                                                         gCATATCCACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGTACGT‑AAAACCTGCAAGGTGGGACCGGATAAGTAGTCAACCTGTG‑ACCATTCTTCGCTGACATCATCCTGGTGGCTGACCACATCACTGaaa                                                                             <  1:84668/149‑1 (MQ=255)                                                                          cATATCCACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGTACGT‑AAAACCTGCAAGGTGGGACCGGATAAGTAGTCAACCTGTG‑ACCATTCTTCGCTGACATCATCCTGGTGGCTGACCACATCACTGAAAcgc                                                                          <  1:274184/151‑1 (MQ=255)                                                                                                cTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGTACCG‑AAAACCCCCCACGGGGGGCCCGATAAAGAGGTAACCCGGGAACCATTC‑TCGCCGGAATCCCCCCGGTGGGCGGACACCACACTGAAACGCGGGGGGGGGGGGGCCTTaaaat                                                    >  1:79828/1‑149 (MQ=255)                                                                                                 tGCCATCCTCGCAGCCATCGGGCGACTGGCGGGGACGT‑AAAACCCGCCAGGGGGGGCCGGGTAAATAGTCAACCTGTG‑ACCATTCTTCCCTGACATCATCCTGGTGGCTGACCACATCACTGAAACGCGGGGGGGGGAGGGCCTTTAAttt                                                   >  2:277102/1‑151 (MQ=255)                                                                                                  gCCATCCTCGCAGCCATCGGGCGACTGGCGGGTACGT‑AAAACCTGCCAGGGGGGACCGGATAAGTAGTCAACCTGGG‑ACCCTTTTTCGCTGACATCATCCTGGTGGGTGACCACATCACTGAAACGCGGGGGGGGGAGGTGCTTAAAttt                                                   >  2:524072/1‑150 (MQ=255)                                                                                                       ccTCGCAGCCATCGGGCGACTGGCGGGTACGT‑AAAACCTGCAAGGTGGGACCGGATAAGTAGTCAACCTGTG‑ACCATTCTTCGCTGACATCATCCTGGTGGCTGACCACATCACTGAAACGCGGTGGGGTGAGGTCCTTAAATTTACTGAt                                             <  2:529697/151‑1 (MQ=255)                                                                                                          cGCAGCCATCGGGCGACTGGCGGGTACGT‑AAAACCTGCAAGGTGGGACCGGATAAGTAGTCAACCTGTG‑ACCATTCTTCGCTGACATCATCCTGGTGGCTGACCACATCACTGAAACGCGGTGGGGTGAGGTCCTTAAATTTACTGATg                                            <  1:62581/149‑1 (MQ=255)                                                                                                                         aCTGGCGGGTACGT‑AAAACCTGCAAGGTGGGACCGGATAAGTAGTCAACCTGTG‑ACCATTCTTCGCTGACATCATCCTGGTGGCTGACCACATCACTGAAACGCGGTGGGGTGAGGTCCTTAAATTTACTGATGGCCTTCAGGTCATCACt                           <  2:275852/151‑1 (MQ=255)                                                                                                                                                  aGGTGGGACCGGATAAGTAGTCAACCTGTG‑ACCATTCTTCGCTGACATCATCCTGGTGGCTGACCACATCACTGAAACGCGGTGGGGTGAGGTCCTTAAATTTACTGATGGCCTTCAGGTCATCACTTCTGTCATCGCATGCGATGAGaa    >  2:561663/1‑150 (MQ=255)                                                                                                                                                     tGGGACCGGATAAGTAGTCAACCTGTG‑ACCATTCTTCGCTGACATCATCCTGGTGGCTGACCACATCACTGAAACGCGGTGGGGTGAGGTCCTTAAATTTACTGATGGCCTTCAGGTCATCACTTCTGTCATCGCATGCGATGAGAAAc  >  1:110432/1‑149 (MQ=255)                                                                                                                                                     |                                                                                                                                                      CCTCCTGGTATTCCAGTTTGATGTTATCGGCAATACACAGCGCATTCATCAGTGGCTGGACGGTTTTTTCCTGCATATCCACGAGGTAGTAGTAACTGCCATCCTCGCAGCCATCGGGCGACTGGCGGGTACGT‑AAAACCTGCAAGGTGGGACCGGATAAGTAGTCAACCTGTG‑ACCATTCTTCGCTGACATCATCCTGGTGGCTGACCACATCACTGAAACGCGGTGGGGTGAGGTCCTTAAATTTACTGATGGCCTTCAGGTCATCACTTCTGTCATCGCATGCGATGAGAAAC  >  NC_000913/266211‑266506

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑