Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,487,155	0	T	A	42.2%	55.0 / 26.9	45	intergenic (+192/‑80)	hrpA/ydcF	putative ATP‑dependent helicase/DUF218 superfamily protein, SAM‑binding
Reads supporting (aligned to +/- strand):  ref base T (6/20);  new base A (19/0);  total (25/20)
Fisher's exact test for biased strand distribution p-value = 7.46e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.17e-01

GGTTTTTTATTAATTCTAAAACGGTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGC‑GG‑TTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTA‑TTATCTCACGCAGTA‑TTC‑TTAAGGGAACGATAAGGA‑GGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGACAGTGGC  >  NC_000913/1487013‑1487304                                                                                                                                                 |                                                                                                                                                          ggTTTTTTATTAATTCTAAAACGGTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGC‑GG‑GTAAAGACATAcaaatt                                                                                                                                                    >  2:1007501/1‑145 (MQ=255)    tttttATTAATTCTAAAACGGTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGC‑GG‑TTTAAGACAAAAGAtttt                                                                                                                                                   >  1:609165/1‑147 (MQ=255)        tattaATTCTAAAACGGTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGC‑GG‑TTAAGGACATACGATTTCCTCCtt                                                                                                                                             <  1:750303/150‑1 (MQ=255)         attaATTCTAAAACGGTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGC‑GG‑TTAAGGACATACGATTTCCTCCTTTc                                                                                                                                           <  2:464353/151‑1 (MQ=255)          ttaATTCTAAAACGGTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGC‑GG‑TTAAAGAAAAAAGATTTTCTCCctt                                                                                                                                            >  1:230355/1‑149 (MQ=255)           taATTCTAAAACGGTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGC‑GG‑TTTAGGAAAAAAAAATTTCTCCtttttt                                                                                                                                         >  1:373505/1‑148 (MQ=255)            aaTTCTAAAACGGTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGC‑GG‑TTTAGGAGATAAGATTTTCTCCttt                                                                                                                                            >  1:239708/1‑147 (MQ=255)             aTTCTAAAACGGTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGC‑GG‑TTAAGGACATACGATTTCCTCCTTTCagag                                                                                                                                       <  2:388034/151‑1 (MQ=255)                  aaaaCGGTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGC‑GG‑TTAAGGACATACGATTTCCTCCTTTCAGAGTGc                                                                                                                                    <  2:475156/149‑1 (MQ=255)                  aaaaCGGTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGC‑GG‑TTAAAGAAAAACGAATTTCTTCTTTCattggggt                                                                                                                                   >  1:548902/1‑143 (MQ=255)                    aaCGGTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGC‑GG‑GTGATGAAAAAAGATTTtctcctctttgtttactc                                                                                                                                  >  2:189160/1‑137 (MQ=255)                                aaaaaTTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGC‑GG‑TTTAAGAAAAAAAAATTTCTCCTTTTAGAGTGGTCCGCTtc                                                                                                                            >  1:993228/1‑143 (MQ=255)                                         ggAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGC‑GG‑TTAATAACAAACTAATTTCTCCTTTTTTTGTGGTCCCCGTCTCCCTA‑TTTtcttccgc                                                                                                          >  2:748476/1‑146 (MQ=255)                                          gAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGC‑GG‑TTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTA‑TTATCTCACGCa                                                                                                         <  2:991627/151‑1 (MQ=255)                                               cAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGC‑GG‑TTAAAGACAATCAAATTTATCCTTTTAGAGGGGGTCGCCTCTCTCTA‑TTTTTTCAcaccgaat                                                                                                     >  2:1135205/1‑143 (MQ=255)                                                aGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGC‑GG‑TTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTA‑TTATCTCACGCAGTA‑TTc                                                                                                  <  2:436950/151‑1 (MQ=255)                                                aGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGC‑GG‑TTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTA‑TTATCTCACGCAGTA‑TTc                                                                                                  <  1:158961/151‑1 (MQ=255)                                                     aaTACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGC‑GG‑TTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTA‑TTATCTCACGCAGTA‑TTC‑TTAAg                                                                                            <  1:809298/151‑1 (MQ=255)                                                         cAATTCTCGGCTGCAAGATGAATGATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGC‑GG‑TTAAGTACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTA‑TTATCTCACGCAGTA‑TTC‑TTAAggg                                                                                          <  2:697795/149‑1 (MQ=255)                                                              ctctGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGC‑GG‑TTTAGGAAAAACAAATTTCTCCTTTCTAAGTGCTCCCCCTCTCCCCC‑TTTTTTCACCCAGGA‑Ttt‑tt                                                                                               >  1:643958/1‑139 (MQ=255)                                                                  gctgcAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGC‑GG‑TTTAGGAAAAAAAAATTTCCCCTTTCTGAATGCTCCCCCTTTCCCTA‑TTTTTTCCCCCCGTA‑TTT‑TTTATGGGAAGATaa                                                                                  >  1:2795/1‑148 (MQ=255)                                                                         gATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGC‑GG‑TTTAAGAAAAAAGAATTTCTCCTTTTCTAGTGGTCCGCCTCTCCCTA‑TTTTTTTCCCCAGAATTTT‑TTAAGGGAA‑GAAAAAGA‑GGaaa                                                                         >  1:869294/1‑148 (MQ=255)                                                                          aTGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGC‑GG‑TTAAAGAAAAAAGAATTTCTCCCTTCTGAGTGGTCCCCCGCTTACTA‑TTATTTTCCCCCGTA‑TTC‑TTTAGGGAAAGATAAAGA‑GGaaa                                                                         >  1:802650/1‑147 (MQ=255)                                                                                 atGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGC‑GG‑TTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTA‑TTATCTCACGCAGTA‑TTC‑TTAAGGGAACGATAAGGA‑GGAACCATGAACAtt                                                               <  2:373492/151‑1 (MQ=255)                                                                                   gTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGC‑GGTTTAAGAAAAAACAATTT‑CTCCTTTTTGAGTGGCCCCCTTCTCACTA‑TTTTTTTACGCCGCA‑TTT‑TTTAAGGAACGAAAAAGA‑AGGAACATGaaaaat                                                               >  1:230828/1‑145 (MQ=255)                                                                                   gTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGC‑GG‑TTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTA‑TTATCTCACGCAGTA‑TTC‑TTAAGGGAACGATAAGGA‑GGAACCATGAACATTa                                                              <  2:776064/150‑1 (MQ=255)                                                                                        tCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGC‑GG‑TTTAAGAAAAACGATTTTCTCCTTTTCGAGTGCTCCCCCTCTCACTA‑TTATTTTACCCCGGATTTT‑TTAAGGGAA‑GATAAAGA‑GGAAACATAAAAATTAtccc                                                          >  1:814933/1‑149 (MQ=255)                                                                                        tCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGC‑GG‑TTTAAGAAAAAAGATTTTCTCCCTTTTGAGAGGCCCCCTTCTCCCTC‑TTTTTTCACCCACGA‑TTT‑TTAATGGGAAGATAAAAA‑GGGAACAAGAACAATAacccc                                                         >  1:1013566/1‑149 (MQ=255)                                                                                           aCAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGC‑GG‑TTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTA‑TTATCTCACGCAGTA‑TTC‑TTAAGGGAACGATAAGGA‑GGAACCATGAACATTACCCCg                                                         <  1:1248774/147‑1 (MQ=255)                                                                                           aCAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGC‑GG‑TTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTA‑TTATCTCACGCAGTA‑TTC‑TTAAGGGAACGATAAGGA‑GGAACCATGAACATTACCCCGtt                                                       <  1:382911/149‑1 (MQ=255)                                                                                              gCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGC‑GG‑TTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTA‑TTATCTCACGCAGTA‑TTC‑TTAAGGGAACGATAAGGA‑GGAACCATGAACATTACCCCGTTTCCGa                                                  <  2:705659/151‑1 (MQ=255)                                                                                                       tAAAAGATATGTCAGGCTTGCGGAGTGGC‑GG‑TTAAAGAAAAAAGATTTTCTCCTTTTTGAGGGCTCCCCCTCTCCCTA‑TTATTTTACCCAGGA‑TTT‑TTTAGGGGAAGAAAAAGAGGGAACCTGAAAAATAACCCCTTTTCCgcg                                                 >  1:151446/1‑142 (MQ=255)                                                                                                        aaaaGATATGTCAGGCTTGCGGAGTGGCGGG‑TTATGAAAAAACAATTTCTCCCTTTCA‑AGGGGTTCCCCTCTTACTA‑TTATCTCACCCCGGATTTT‑TTAAGGGAA‑GACAAAGAGGGAACCA‑CAACATTAACCCCCTTcccgcgcc                                              >  1:262779/1‑139 (MQ=255)                                                                                                         aaaGATATGTCAGGCTTGCGGAGTGGC‑GG‑TTAAAGAAAAAAGATTTTCTTCCTTCTAAGTGCTCCCCCTCTCCCTATTTTTTTCAC‑CAGTC‑TTCTTTAAGGGAA‑GAGAAAGA‑GGAAACAAGAACAATAACCCCCTTcccccccttttccc                                        >  1:474334/1‑138 (MQ=255)                                                                                                          aaGATATGTCAGGCTTGCGGAGTGGC‑GG‑TTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTA‑TTATCTCACGCAGTA‑TTC‑TTAAGGGAACGATAAGGA‑GGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCgg                                      <  2:211321/151‑1 (MQ=255)                                                                                                            gATATGTCAGGCTTGCGGAGTGGC‑GG‑TTAAGGAAAAAAAATTTTCTCCTTTCTGAGGGCTCCCCCTCCTCCTA‑TTATTTCCCCCAGGA‑TTT‑TTTATGGGAAGATAAAGA‑GGAAACCAAAAAAATACCCCCCTTCCGCCGCTTTTGcc                                        >  1:54109/1‑147 (MQ=255)                                                                                                                      gCTTGCGGAGTGGC‑GG‑TTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTA‑TTATCTCACGCAGTA‑TTC‑TTAAGGGAACGATAAGGA‑GGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATg                          <  1:497280/151‑1 (MQ=255)                                                                                                                         tGCGGAGTGGC‑GG‑TTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTA‑TTATCTCACGCAGTA‑TTC‑TTAAGGGAACGATAAGGA‑GGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGc                         <  1:988056/149‑1 (MQ=255)                                                                                                                                  gC‑GG‑TTAAGGACATACGCTTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTA‑TTATCTCACGCAGTA‑TTC‑TTAAGGGAACGATAAGGA‑GGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAACTGtt               >  2:409763/1‑150 (MQ=255)                                                                                                                                          aaGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTA‑TTATCTCACGCAGTA‑TTC‑TTAAGGGAACGATAAGGA‑GGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGAc        >  1:577010/1‑151 (MQ=255)                                                                                                                                           aGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTA‑TTATCTCACGCAGTA‑TTC‑TTAAGGGAACGATAAGGA‑GGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGACa       <  2:609148/151‑1 (MQ=255)                                                                                                                                            ggACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTA‑TTATCTCACGCAGTA‑TTC‑TTAAGGGAACGATAAGGA‑GGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGAc        >  1:651272/1‑149 (MQ=255)                                                                                                                                             gACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTA‑TTATCTCACGCAGTA‑TTC‑TTAAGGGAACGATAAGGA‑GGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGACAGt     <  2:2795/151‑1 (MQ=255)                                                                                                                                              aCATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTA‑TTATCTCACGCAGTA‑TTC‑TTAAGGGAACGATAAGGA‑GGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGACAGtg    <  1:984750/151‑1 (MQ=255)                                                                                                                                               cATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTA‑TTATCTCACGCAGTA‑TTC‑TTAAGGGAACGATAAGGA‑GGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGACAGtgg   >  2:584293/1‑151 (MQ=255)                                                                                                                                                 tACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTA‑TTATCTCACGCAGTA‑TTC‑TTAAGGGAACGATAAGGA‑GGAACCATGAACATTACCCCTTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGACAGtggc  <  2:642897/150‑1 (MQ=255)                                                                                                                                                 |                                                                                                                                                          GGTTTTTTATTAATTCTAAAACGGTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGC‑GG‑TTAAGGACATACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTA‑TTATCTCACGCAGTA‑TTC‑TTAAGGGAACGATAAGGA‑GGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGACAGTGGC  >  NC_000913/1487013‑1487304

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑