Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,487,153	0	C	A	42.9%	75.1 / 21.5	42	intergenic (+190/‑82)	hrpA/ydcF	putative ATP‑dependent helicase/DUF218 superfamily protein, SAM‑binding
Reads supporting (aligned to +/- strand):  ref base C (2/22);  new base A (18/0);  total (20/22)
Fisher's exact test for biased strand distribution p-value = 5.37e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCGGGTTTTTTATTAATTCTAAAACGGTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTA‑TTCTTA‑AGGGAACGATAAGGAGGAACCATGAACATTAC‑CCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGACAG  >  NC_000913/1487010‑1487300                                                                                                                                                 |                                                                                                                                                       ccGGGTTTTTTATTAATTCTAAAACGGTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAGGACATACGAt                                                                                                                                                 <  2:547835/151‑1 (MQ=255)           tattaATTCTAAAACGGTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTTAAGAAATaaaatattcttcttt                                                                                                                                       >  2:476283/1‑137 (MQ=255)            attaATTCTAAAACGGTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAAGACATAAAATTTTCTCCttt                                                                                                                                       >  2:221581/1‑150 (MQ=255)                aTTCTAAAACGGTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAGGACATACGATTTCCTCCTTTCagag                                                                                                                                  <  2:709380/151‑1 (MQ=255)                aTTCTAAAACGGTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAGGAAAAACGATTTTCTCCttt                                                                                                                                       >  1:390196/1‑146 (MQ=255)                    tAAAACGGTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAGGAAAAAAAAATTCCTCCTTTCagagggg                                                                                                                               >  1:381847/1‑147 (MQ=255)                      aaaCGGTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAGGACATACGATTTCCTCCTTTCAGAGTGCTcc                                                                                                                            <  2:1069035/151‑1 (MQ=255)                      aaaCGGTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAGGACATACGATTTCCTCCTTTCAGAGTGCTcc                                                                                                                            <  1:39694/151‑1 (MQ=255)                           gTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTtc                                                                                                                       <  2:589574/151‑1 (MQ=255)                             aaGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAGGACATACGATTTCCTCCTTTCAGAGTGCCCCGCTtctc                                                                                                                     <  2:152041/151‑1 (MQ=255)                                          cAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTTAAGAAAAAAGAATTTCTCCTTTTTTAGGGCTCCGCCTCTCCCcattattt                                                                                                           >  1:259707/1‑146 (MQ=255)                                          cAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCAc                                                                                                        <  1:1168549/151‑1 (MQ=255)                                             gAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAAGAAAAAAGACTTTCTCCTTTTCGAGTGGGCCGCTtctccccactatttctccc                                                                                                      >  1:114021/1‑135 (MQ=255)                                                   aGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTA‑TTc                                                                                              <  2:656480/151‑1 (MQ=255)                                                    gAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAAAAAAAACAAATTTTTCCCTTTATAGTGGGCCCCCTTTCCCTATTTTTTCACTCAGTA‑tttt                                                                                             >  2:222840/1‑149 (MQ=255)                                                        aaTACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTTAAGAAATAAGAATTTCTCCCTTTTCAGTGGTCCCCTTCTCTCTATTTTTTCCCGCCGTA‑Ttttt                                                                                            >  1:536523/1‑148 (MQ=255)                                                          tACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAAGAAAAACGATTTTCTCCTTTTTTAGGGCTCCGCTTCTCCCTATTATTTCACGCCGGA‑Ttttttaagg                                                                                       >  1:1163453/1‑146 (MQ=255)                                                           aCAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTA‑TTCTTA‑AGGGa                                                                                     <  1:124375/151‑1 (MQ=255)                                                             aaTTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTA‑TTCTTA‑AGGGAAc                                                                                   <  2:745411/151‑1 (MQ=255)                                                                  tctGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTTAAGAAAAAAGAATTTTTTCTTTTTGAGTGCTCCGCTTCTCACTATTTTTTCACCCCATA‑TTTTTT‑Aggggaagaaa                                                                               >  2:554236/1‑143 (MQ=255)                                                                     gctgcAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTA‑TTCTTA‑AGGGAACGATaa                                                                              <  1:1177428/148‑1 (MQ=255)                                                                     gctgcAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTA‑TTCTTA‑AGGGAACGATAagga                                                                           <  1:433054/151‑1 (MQ=255)                                                                             aTGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTA‑TTCTTA‑AGGGAACGATAAGGAGGAACCAt                                                                   <  2:171084/151‑1 (MQ=255)                                                                               gAAAAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTA‑TTCTTA‑AGGGAACGATAAGGAGGAACCATGa                                                                 <  1:552578/151‑1 (MQ=255)                                                                                aataatGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTTAAGACATAAGAATTTCTCCTTTTCGAGTGCTCCCCCTCTCCCTTTTTTCTCTCGCAGTA‑TTCTTT‑AAGGGACGATAaagaggga                                                                       >  1:193311/1‑142 (MQ=255)                                                                                   aatGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTA‑TTCTTA‑AGGGAACGATAAGGAGGAACCATGAACAt                                                             <  1:959105/151‑1 (MQ=255)                                                                                   aatGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAAGAAAAAAAATTTTCTTCTTTCTTAGTGGTCCCCTTCTCTCTATTATTTCACCCCATA‑TTCTTT‑AGGGGAAGAAAAAGAGGGACCATTaaaa                                                              >  2:533692/1‑148 (MQ=255)                                                                                      gTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTA‑TTCTTA‑AGGGAACGATAAGGAGGAACCATGAACATTa                                                           <  1:1131946/150‑1 (MQ=255)                                                                                         tATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTA‑TTCTTA‑AGGGAACGATAAGGAGGAACCATGAACATTAc‑cc                                                       <  2:234224/150‑1 (MQ=255)                                                                                              aCAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAAGAAATAAAAATTTTTTCTTTTTGAGGGGTCCGCCTTTCCCATTTTTTTCTCGCCGAA‑ATTTTT‑AGGGGACCATAAGGAAGAAACATGAAAATTACACCCGtt                                                   >  2:350125/1‑150 (MQ=255)                                                                                              aCAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑GTAATGAAAAACCAATTTCTCCTTTTTGAGTGGTCCGCCTCTCCCTATTTTCTTCCGCAGGA‑TTTTTT‑TAGGAAAGATAAGGAGGAAACCTGAAAAtattccccctt                                                   >  2:1205950/1‑140 (MQ=255)                                                                                                aGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTTAAGAAAAAACAATTT‑CTCCCTTCTGAGGGGTCCCCCTCTCTCTATTATTTCACGCAGGATTTTTTA‑AGGGAA‑GATAAAGAGGAAACAAGAAAAATAa‑ccc                                                      >  1:1177444/1‑144 (MQ=255)                                                                                                aGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTA‑TTCTTA‑AGGGAACGATAAGGAGGAACCATGAACATTAC‑CCCGTTTCCg                                               <  2:181735/151‑1 (MQ=255)                                                                                                 gCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAGGAAAAAAGAATTTCTCCCTTTAGAGTGCTCCGCCTCTCCCTCTTATCTCACCCAGGA‑TTTTTATAGGGAA‑GAAAAAGAGGAAACACGAACAATAC‑CCCCttt                                                  >  1:183850/1‑147 (MQ=255)                                                                                                  cATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTA‑TTCTTA‑AGGGAACGATAAGGAGGAACCATGAACATTAC‑CCCGTTTCCGAc                                             <  1:147503/151‑1 (MQ=255)                                                                                                      tCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAGGAAAAACGATTTTCTTCTTTTCGAGGGCGCCCCCTCTCACTATTATTTCCCCCCAGA‑TTTTTA‑AGGGGAAGGTAAGGAGGAACCCAGAAACTTAA‑CCCCGTTCCGCCCCtt                                         >  1:205065/1‑151 (MQ=255)                                                                                                         ttAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAAGAAATACAATTTCCTCCTTTCAGAGTGCTCCGCCTCTCCCTATTTTCTCACGCAGTA‑TTCTTT‑AAGGGACGCAAAGGAGGGACCATAAAAAATAA‑CCCACTTCCGACGCTTTc                                       >  2:352387/1‑150 (MQ=255)                                                                                                             aaGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAAGAAAAACGATTTTCTCCCTTCAGAGAGCTCCCCTTCTCCCTATTTTTTCACCCAGGG‑TTTTTT‑AGGGGACGAAAAAGAGGAAACCAGAAAATTACTCCCCTTTCCG‑CGCTTTCGcc                                    >  1:908492/1‑149 (MQ=255)                                                                                                                atatGTCAGGCTTGCGGAGTGGCGG‑TTAAAGAAATACGAATTTCTTCTTTCTTTGGGGTCCCCCTTTCACCTTTTTTTTACGCAGGA‑TTTTTA‑AGGGAACGATAAGGAGGGAACATGAAAAATAC‑CCCCTTTTCGCCGCCTTTGCCGGc                                 >  2:945821/1‑149 (MQ=255)                                                                                                                      cAGGCTTGCGGAGTGGCGG‑TTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTA‑TTCTTA‑AGGGAACGATAAGGAGGAACCATGAACATTAC‑CCCGTTTCCGACGCTTTCGCCGGCAACtata                          <  1:394865/150‑1 (MQ=255)                                                                                                                               ggAGTGGCGG‑TTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTA‑TTCTTA‑AGGGAACGATAAGGAGGAACCATGAACATTAC‑CCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATaa                <  2:176712/151‑1 (MQ=255)                                                                                                                                              ggACATACGATTTCCTCCTTTCGGAGTGCTCTGCTTCTCACTATTATCTCACGCAGTA‑TTATTA‑AGGGAACGATAAGGGGGAACCATGACCATTAC‑CCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGACAg  <  2:796418/151‑1 (MQ=255)                                                                                                                                                 |                                                                                                                                                       CCGGGTTTTTTATTAATTCTAAAACGGTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGG‑TTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCACGCAGTA‑TTCTTA‑AGGGAACGATAAGGAGGAACCATGAACATTAC‑CCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGACAG  >  NC_000913/1487010‑1487300

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑