Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,332,309	0	A	C	42.2%	66.1 / 21.4	45	L322V (TTA→GTA)	basS	sensory histidine kinase in two‑component regulatory system with BasR
Reads supporting (aligned to +/- strand):  ref base A (20/6);  new base C (0/19);  total (20/25)
Fisher's exact test for biased strand distribution p-value = 7.46e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCTGGTGGTCAGCAGCTTTCTTTATATCTGGTTTGCCACGTACTGATCTTTCTTCAGCCGTACCCAGGCCCGCGTGCCGGAAGTCTCTTGCCGGTTTT‑GCAGGAAAAA‑CTGCCC‑GTGATGCAACT‑GTGTAATG‑CGGCTGACAATACTTAACCCCAGACC‑AATCCCGCCATAACGGCTGTCCATACGTACAAACGCTTTACTCAACTCCCCGCATTTACTCTCATCAATACCTGGTCCTTCATCTTCAACTGCCATGACCGCTCCGTCATCTTCTTGCAGCTTAATCAT  >  NC_000913/4332160‑4332447                                                                                                                                                           |                                                                                                                                            gCTGGTGGTCAGCAGCTTTCTTTATATCTGGTTTGCCACGTACTGATCTTTCTTCAGCCGTACCCAGGCCCGCGTGCCGGAAGTCTCTTGCCGGTTTT‑GCAGGAAAAA‑CTGCCC‑GTGATGCAACT‑GTGTAATG‑CGGCTGACAATACTTAAc                                                                                                                                            >  2:134733/1‑151 (MQ=255)  cTGGTGGTCAGCAGCTTTCTTTATATCTGGTTTGCCACGTACTGATCTTTCTTCAGCCGTACCCAGGCCCGCGTGCCGGAAGTCTCTTGCCGGTTTT‑GCAGGAAAAA‑CTGCCC‑GTGATGCAACT‑GTGTAATG‑CGGCTGACAATACTTAAcc                                                                                                                                           >  1:417433/1‑151 (MQ=255)    ggtggtCAGCAGCTTTCTTTATATCTGGTTTGCCACGTACTGATCTTTCTTCAGCCGTACGCAGGCCCGCGTGCCGGAAGTCTCTTGCCGGTTTT‑GCAGGAAAAA‑CTGCCC‑GTGATGCAACT‑GTGTAATG‑CGGCTGACAATACTTAAcccc                                                                                                                                         <  1:285895/151‑1 (MQ=255)    ggtggtCAGCAGCTTTCTTTATATCTGGTTTGCCACGTACTGATCTTTCTTCAGCCGTACCCAGGCCCGCGTGCCGGAAGTCTCTTGCCGGTTTT‑GCAGGAAAAA‑CTGCCC‑GTGATGCAACT‑GTGTAATG‑CGGCTGACAATACTTAAcc                                                                                                                                           <  2:188682/149‑1 (MQ=255)        gtCAGCAGCTTTCTTTATATCTGGTTTGCCACGTACTGATCTTTCTTCAGCCGTACCCAGGCCCGCGTGCCGGAAGTCTCTTGCCGGTTTT‑GCAGGAAAAA‑CTGCCC‑GTGATGCAACT‑GTGTAATG‑CGGCTGACAATACTTAACCCCAGAc                                                                                                                                     <  1:352632/151‑1 (MQ=255)          cagcagCTTTCTTTATATCTGGTTTGCCACGTACTGATCTTTCTTCAGCCGTACCCAGGCCCGCGTGCCGGAAGTCTCTTGCCGGTTTT‑GCAGGAAAAA‑CTGCCC‑GTGATGCAACT‑GTGTAATG‑CGGCTGACAATACTTAACCCCAGACC‑a                                                                                                                                  <  1:861000/151‑1 (MQ=255)             cagcTTTCTTTATATCTGGTTTGCCACGTACTGATCTTTCTTCAGCCGTACCCAGGCCCGCGTGCCGGAAGTCTCTTGCCGGTTTT‑GCAGGAAAAA‑CTGCCC‑GTGATGCAACT‑GTGTAATG‑CGGCTGACAATACTTAACCCCAGACC‑AATc                                                                                                                               <  2:906334/151‑1 (MQ=255)               gcTTTCTTTATATCTGGTTTGCCACGTACTGATCTTTCTTCAGCCGTACCCAGGCCCGCGTGCCGGAAGTCTCTTGCCGGTTTT‑GCAGGAAAAA‑CTGCCC‑GTGATGCAACT‑GTGTAATG‑CGGCTGACAATACTTAACCCCAGACC‑AATccc                                                                                                                             >  2:839873/1‑151 (MQ=255)                         tatCTGGTTTGCCACGTACTGATCTTTCTTCAGCCGTACCCAGGCCCGCGTGCCGGAAGTCTCTTGCCGGTTTT‑GCAGGAAAAA‑CTGCCC‑GTGATGCAACT‑GTGTAATG‑CGGCTGACAATACTTAACCCCAGACC‑AATCCCGCCATAACg                                                                                                                    >  2:628930/1‑150 (MQ=255)                                    ccACGTACTGATCTTTCTTCAGCCGTACCCAGGCCCGCGTGCCGGAAGTCTCTTGCCGGTTTT‑GCAGGAAAAA‑CTGCCC‑GTGATGCAACT‑GTGTAATG‑CGGCTGACAATACTTAACCCCAGACC‑AATCCCGCCATAACGGCTGTCCATACg                                                                                                        >  2:185506/1‑151 (MQ=255)                                     cactttctgttttttctcCAGCCGTCCCCAGGCCCGCTCGCCGAAAGTCT‑TTTCCGGTTTTGGCAAAAAACC‑CCCCCC‑GGGATCCAATG‑GTAAAATG‑CGTGTAAAAATCTTTACCCCAACCCC‑AACCCCGCCATAACGGCTGTCCATACGt                                                                                                       <  1:451880/139‑1 (MQ=255)                                             gtttttcctccccccGTCCCCGGCCCCGGGTGCCGGATGTCT‑TTGGCTGTTTT‑AGAAGAAAAA‑CCGCCCGGTGACCCACTT‑GTGTAGGG‑CGTTTAACAATATTTACCCCCAGACC‑AACCCCGCCATAACGGCTGTCCATACGTACaa                                                                                                   <  1:226821/134‑1 (MQ=255)                                              ttttttcttagtccGTCCCCGGCCCCGGGCGCGGGATTTCTCTTGCGGTTTTC‑GCAAAAAAAG‑CTGCCG‑ATGATGCATTT‑GTAAAATG‑GGGCAAAAAATACTAACCCCAAGCCC‑ATCCCCGCCATAACGGCTGTCCATACGTACAAAc                                                                                                 <  1:637505/136‑1 (MQ=255)                                              aTCTTTCTTCAGCCGTACCCAGGCCCGCGTGCCGGAAGTCTCTTGCCGGTTTT‑GCAGGAAAAA‑CTGCCC‑GTGATGCAACT‑GTGTAATG‑CGGCTGACAATACTTAACCCCAGACC‑AATCCCGCCATAACGGCTGTCCATACGTACAAACGCt                                                                                              >  1:51454/1‑151 (MQ=255)                                              aTCTTTCTTCAGCCGTACCCAGGCCCGCGTGCCGGAAGTCTCTTGCCGGTTTT‑GCAGGAAAAA‑CTGCCC‑GTGATGCAACT‑GTGTAATG‑CGGCTGACAATACTTAACCCCAGACC‑AATCCCGCCATAACGGCTGTCCATACGTACAAACGCt                                                                                              >  1:235402/1‑151 (MQ=255)                                               tctttcttCAGCCGTACCCAGGCCCGCGTGCCGGAAGTCTCTTGCCGGTTTT‑GCAGGAAAAA‑CTGCCC‑GTGATGCAACT‑GTGTAATG‑CGGCTGACAATACTTAACCCCAGACC‑AATCCCGCCATAACGGCTGTCCATACGTACAAACGCtt                                                                                             >  1:790905/1‑151 (MQ=255)                                                ctttcttCAGCCGTACCCAGGCCCGCGTGCCGGAAGTCTCTTGCCGGTTTT‑GCAGGAAAAA‑CTGCCC‑GTGATGCAACT‑GTGTAATG‑CGGCTGACAATACTTAACCCCAGACC‑AATCCCGCCATAACGGCTGTCCATACGTACAAACGCttt                                                                                            >  1:101349/1‑151 (MQ=255)                                                  ttctccccccGTCCCCGGCCCCGGGTGCGGAATTTTTCTTGCGTGTTTT‑GAAGAAAAAC‑CGCCCC‑GTGATCAACCT‑GTGTAATG‑GGGATAACAATATTACCCCCCACACA‑AATCCCGCCATAACGGCTGTCCATACGTACAAACGCtt                                                                                             <  1:669842/140‑1 (MQ=255)                                                          ccgcccccggccccGCGTGCAGGAAGTCTCTTGCCGTTTTT‑GCAGAAAAAC‑CCCCCC‑GGAATCCATCT‑GTGAAATG‑CGGCAGAAAATACTAACCCCAAAACC‑AACCCCGCCATAACGGCTGTCCATACGTACAAACGCTTTACTCAACt                                                                                    <  1:213733/138‑1 (MQ=255)                                                          ccccccccGGGCCCGCGTGCGGGAATTCTCTTGCGGTTTTA‑GAAAAAAAAC‑CCCCCC‑GTGATGAACTT‑GTGAAAGG‑GGGCTAAAATTACTCACCCCCACCCC‑ACCCCCGCCATAACGGCTGTCCATACGTACAAACGCTTTACTCAAc                                                                                     <  2:336827/143‑1 (MQ=255)                                                           cGTACCCAGGCCCGCGTGCCGGAAGTCTCTTGCCGGTTTT‑GCAGGAAAAA‑CTGCCC‑GTGATGCAACT‑GTGTAATG‑CGGCTGACAATACTTAACCCCAGACC‑AATCCCGCCATAACGGCTGTCCATACGTACAAACGCTTTACTCAACTccc                                                                                 >  2:258480/1‑151 (MQ=255)                                                              ccccggccccGCGTGCAGGAATTCTCTGGCGGTTTTT‑GAAGAAAAAC‑CCCCCG‑GTGAT‑CAACTGGGGAAAGG‑CGTCTAAAAAT‑CCTAACCCCAACCCAAATCCCGCCATAACGGCTGTCCATACGTACAAACGCTTTACTCAACTcccc                                                                                <  1:808352/142‑1 (MQ=255)                                                               cccggccccGCGTGCGGAAAGTCTTTTGCGGTTTTT‑GAAGAAAAAC‑CTCCCG‑GTGATGCAACT‑GTGTAAGG‑CGGCTAAAAATACTAACCCCCAGCCA‑AACCCCGCCATAACGGCTGTCCATACGTACAAACGCTTTACTCAACTCCCCGc                                                                              <  1:134747/144‑1 (MQ=255)                                                                   gccccGCGTGCCGAATTTCTCTTGCCGTTTTG‑GCAAAAAACC‑CCCCCG‑GTGGTCCACCT‑GTGAAAGG‑GGGCTAAAAATACTTCCCCCCACCCC‑CCCCCCGCCATAACGGCTGTCCATACGTACAAACGCTTTACTCAACTCCCCGCAtt                                                                           <  2:349278/147‑1 (MQ=255)                                                                     ccggcgTGCCGAAAGTCTCTTG‑CGGTTTT‑GGAAAAAAAACCTCCCC‑GTGATCCATCT‑GTTTAAGG‑CGGCTAAAAATACTAACCCCAACCCC‑AACCCCGCCATAACGGCTGTCCATACGTACAAACGCTTTACTCAACTCCCCGCATTTAc                                                                        <  1:686009/147‑1 (MQ=255)                                                                           ggcggaaaGTCT‑TTGCCCGTTTT‑GGAAGAAAAACCGGCCC‑GTGATGCATTT‑GTGAAATG‑CGTCTAAAAATACTAACCCCCAGACA‑AACCCCGCCATAACGGCTGTCCATACGTACAAACGCTTTACTCAACTCCCCGCATTTACtctc                                                                    <  1:435846/142‑1 (MQ=255)                                                                             ccGGAGTTCTCTTGCCGTTTTT‑CAAGAAAAAC‑CCGCCC‑GAGATGAATTT‑GTATATTG‑CGGCTAAAAATCCTAACCCCCACACC‑AACCCCGCCATAACGGCTGTCCATACGTACAAACGCTTTACTCAACTCCCCGCATTTACTCtcat                                                                  <  1:930979/148‑1 (MQ=255)                                                                              cGGAATTCTCTTGCGGGTTTT‑GAAGAAAAAC‑CTCCCC‑GTAATGCAACT‑TTGTAATG‑CGGCTAACAATACTCACCCCCACACC‑AACCCCGCCATAACGGCTGTCCATACGTACAAACGCTTTACTCAACTCCCCGCATTTACTCTCATCAAt                                                              <  1:345194/151‑1 (MQ=255)                                                                               ggAATTCTTTGGCGGGTTTT‑GGAAAAAAAC‑CTCCCC‑GTGATACATGT‑TGGAAGTG‑GGGCTAACAATCCCAACCCCCAACCA‑AATCCCGCCATAACGGCTGTCCATACGTACAAACGCTTTACTCAACTCCCCGCATTTACTCtcatca                                                                <  1:835616/148‑1 (MQ=255)                                                                                gAAGTCTCTTGCTGGTTTT‑GAAAAAAAAC‑CGCCCC‑GTAATCCAA‑T‑GTTGAAGGCCGGCTAAAACAACTAACCCCCAGCCC‑ACCCCCGCCATAACGGCTGTCCATACGTACAAACGCTTTACTCAACTCCCCGCATTTACTCtcatc                                                                 <  2:559187/146‑1 (MQ=255)                                                                                        ttGCCGGTTTT‑GCAGGAAAAA‑CTGCCC‑GTGATGCAACT‑GTGTAATG‑CGGCTGACAATACTTAACCCCAGACC‑AATCCCGCCATAACGGCTGTCCATACGTACAAACGCTTTACTCAACTCCCCGCATTTACTCTCATCAATACCTGGTCCt                                                    >  1:774084/1‑151 (MQ=255)                                                                                         tggcGGTTTT‑GGAAGAAAAACCTCCCC‑GTGACGAATCT‑GTTTAAGG‑GGACTAAAAATCCTTACCCCCACCCA‑AACCCCGCCATAACGGCTGTCCATACGTACAAACGCTTTACTCAACTCCCCGCATTTACTCTCATCAATACCTgg                                                        <  2:938850/144‑1 (MQ=255)                                                                                          gCCGGTTTT‑GCAGGAAAAA‑CTGCCC‑GTGATGCAACT‑GTGTAATG‑CGGCTGACAATACTTAACCCCAGACC‑AATCCCGCCATAACGGCTGTCCATACGTACAAACGCTTTACTCAACTCCCCGCATTTACTCTCATCAATACCTGGTCCtt                                                   >  1:806684/1‑150 (MQ=255)                                                                                           cgggTTTT‑GCAGAAAAAC‑CTGCCG‑GTAAAACATCT‑GTGTAAGG‑GGTCCAAAAATACAACCCCCCACCCC‑AACCCCGCCATAACGGCTGTCCATACGTACAAACGCTTTACTCAACTCCCCGCATTTACTCTCATCAATACCTGGTcc                                                     <  1:329418/145‑1 (MQ=255)                                                                                            cGGTTTT‑GCAGGAAAAA‑CTGCCC‑GTGATGCAACT‑GTGTAATG‑CGGCTGACAATACTTAACCCCAGACC‑AATCCCGCCATAACGGCTGTCCATACGTACAAACGCTTTACTCAACTCCCCGCATTTACTCTCATCAATACCTGGTCCTTCAt                                                >  1:501660/1‑151 (MQ=255)                                                                                             ggTTTT‑GCAGGAAAAA‑CTGCCC‑GTGATGCAACT‑GTGTAATG‑CGGCTGACAATACTTAACCCCAGACC‑AATCCCGCCATAACGGCTGTCCATACGTACAAACGCTTTACTCAACTCCCCGCATTTACTCTCATCAATACCTGGTCCTTCATc                                               >  1:911315/1‑151 (MQ=255)                                                                                              gttttggcaaaaaaac‑CTCCCC‑GTGTTCAAATT‑GTGTAAGG‑GGGCTAACAACCCTCACCCCCACCCC‑ACCCCCGCCATAACGGCTGTCCATACGTACAAACGCTTTACTCAACTCCCCGCATTTACTCtcatca                                                                <  2:854459/123‑1 (MQ=255)                                                                                                           aaaaccccccggtaaTGCATTT‑GTTTAATG‑GGGCAAAAAATCCTCACCCCCAGCCC‑AATCCCGCCATAACGGCTGTCCATACGTACAAACGCTTTACTCAACTCCCCGCATTTACTCTCATCAATACCTGGTCCTTCATCTTCAAc                                         <  2:153984/132‑1 (MQ=255)                                                                                                                  ccc‑GTGTTGCAATT‑GGGAAATG‑GGCCTAAAAATCCTAACCCCCACCCC‑AACCCCGCCATAACGGCTGTCCATACGTACAAACGCTTTACTCAACTCCCCGCATTTACTCTCATCAATACCTGGTCCTTCATCTTCAACTGCCATGAcc                               <  1:810949/148‑1 (MQ=255)                                                                                                                      gTGATGCAACT‑GTGTAATG‑CGGCTGACAATACTTAACCCCAGACC‑AATCCCGCCATAACGGCTGTCCATACGTACAAACGCTTTACTCAACTCCCCGCATTTACTCTCATCAATACCTGGTCCTTCATCTTCAACTGCCATGACCGCTCCg                         >  1:47306/1‑151 (MQ=255)                                                                                                                           gCAACT‑GTGTAATG‑CGGCTGACAATACTTAACCCCAGACC‑AATCCCGCCATAACGGCTGTCCATACGTACAAACGCTTTACTCAACTCCCCGCATTTACTCTCATCAATACCTGGTCCTTCATCTTCAACTGCCATGACCGCTCCGTCAtc                    >  1:133141/1‑151 (MQ=255)                                                                                                                             aaCT‑GTGTAATG‑CGGCTGACAATACTTAACCCCAGACC‑AATCCCGCCATAACGGCTGTCCATACGTACAAACGCTTTACTCAACTCCCCGCATTTACTCTCATCAATACCTGGTCCTTCATCTTCAACTGCCATGACCGCTCCGTCAtctt                  >  1:651512/1‑151 (MQ=255)                                                                                                                                         g‑CGGCTGACAATACTTAACCCCAGACC‑AATCCCGCCATAACGGCTGTCCATACGTACAAACGCTTTACTCAACTCCCCGCATTTACTCTCATCAATACCTGGTCCTTCATCTTCAACTGCCATGACCGCTCCGTCATCTTCTTGCAGCtt        >  1:22183/1‑150 (MQ=255)                                                                                                                                           cGGCTGACAATACTTAACCCCAGACC‑AATCCCGCCATAACGGCTGTCCATACGTACAAACGCTTTACTCAACTCCCCGCATTTACTCTCATCAATACCTGGTCCTTCATCTTCAACTGCCATGACCGCTCCGTCATCTTCTTGCAGCTTa       >  1:917163/1‑150 (MQ=255)                                                                                                                                                gACAATACTTAACCCCAGACC‑AATCCCGCCATAACGGCTGTCCATACGTACAAACGCTTTACTCAACTCCCCGCATTTACTCTCATCAATACCTGGTCCTTCATCTTCAACTGCCATGACCGCTCCGTCATCTTCTTGCAGCTTAATCAt  >  2:852703/1‑150 (MQ=255)                                                                                                                                                           |                                                                                                                                            GCTGGTGGTCAGCAGCTTTCTTTATATCTGGTTTGCCACGTACTGATCTTTCTTCAGCCGTACCCAGGCCCGCGTGCCGGAAGTCTCTTGCCGGTTTT‑GCAGGAAAAA‑CTGCCC‑GTGATGCAACT‑GTGTAATG‑CGGCTGACAATACTTAACCCCAGACC‑AATCCCGCCATAACGGCTGTCCATACGTACAAACGCTTTACTCAACTCCCCGCATTTACTCTCATCAATACCTGGTCCTTCATCTTCAACTGCCATGACCGCTCCGTCATCTTCTTGCAGCTTAATCAT  >  NC_000913/4332160‑4332447

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑