Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,487,163	0	C	T	45.0%	36.2 / 19.6	41	intergenic (+200/‑72)	hrpA/ydcF	putative ATP‑dependent helicase/DUF218 superfamily protein, SAM‑binding
Reads supporting (aligned to +/- strand):  ref base C (2/20);  new base T (18/0);  total (21/20)
Fisher's exact test for biased strand distribution p-value = 3.35e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.92e-01

TATTAATTCTAAAACGGTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACA‑TACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCA‑CGCAGTA‑TTCTTAAGGGAACGATAAGGA‑GGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGACAGTGGCTGGCGCAGG  >  NC_000913/1487020‑1487313                                                                                                                                                 |                                                                                                                                                          tattaATTCTAAAACGGTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAAGAAA‑AAAAATTTTCCCCttt                                                                                                                                                    >  1:18286/1‑151 (MQ=255)           aaaaAGGTAAGGGTAAAAAATCAGGAAATCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAACGATATTTCATTCTTGCTGAATGGCGTTTAATCACA‑TACAAATTCCTCTTTTAagaga                                                                                                                                              <  2:368100/147‑2 (MQ=255)            aaaCGGTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACA‑TACGATTTCCTCCTTTCAGAGTGCTcc                                                                                                                                         <  1:622626/151‑1 (MQ=255)             aaCGGTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTTAGGAAA‑AAAAAATTTCTCCtttttgaatgcccc                                                                                                                                         >  1:433405/1‑139 (MQ=255)              aCGGTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTTAAGAAA‑AAAGATTTTCTTCCTTTAGAGTg                                                                                                                                             >  1:327855/1‑145 (MQ=255)               cGGTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACA‑TACGATTTCCTCCTTTCAGAGTGCTCCGCt                                                                                                                                      <  2:525847/151‑1 (MQ=255)                   aaGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACA‑TACGATTTCCTCCTTTCAGAGTGCTCCGCTtct                                                                                                                                   <  2:289209/150‑1 (MQ=255)                         aaaaaTTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTTAAGAAA‑AACGATTTTCTTCCTTTTGAGTGGTCCGCTtct                                                                                                                                   >  1:546899/1‑144 (MQ=255)                           ataTTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACA‑TACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACtattat                                                                                                                          <  1:769926/149‑1 (MQ=255)                           aaaTTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAAGAAA‑AAAGATTTTCTCCTTTTAGAGTGGTCCGCCTCTCACcattat                                                                                                                          >  1:144758/1‑151 (MQ=255)                            aaTTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACA‑TACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTAtc                                                                                                                         <  1:211612/151‑1 (MQ=255)                                 aGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTGCCTTAAAAGAGATGTCAGGCTTGCGGAGTGGCGGTTAAGGACA‑TACTATGTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCA‑Cg                                                                                                                   <  2:570838/151‑1 (MQ=255)                                       tCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACA‑TACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCA‑CGCAGTa                                                                                                              <  1:77613/150‑1 (MQ=255)                                            aaaaTACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAATTACA‑TAAAAAATTTTCCTTTTTTAGGGGTCCGCTTCTCTCCATTATCTCA‑CCCAGCA‑Ttttt                                                                                                        >  2:19104/1‑150 (MQ=255)                                                   aaTTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTTAAGACA‑TAAAATTTTTTCCTTTTTGAGTGCTCCCCGTTTCTCTATTTTTTCA‑CTCCGTA‑Tttttttagg                                                                                                   >  2:10610/1‑143 (MQ=255)                                                    aTTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGAAA‑TAAAATTTTTTTCTTTCTTAGGGCTCCACTTCTCCCAATTTTCTCA‑CCCCGTA‑TTCtttatgggac                                                                                                >  2:729536/1‑142 (MQ=255)                                                     ttCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTTAAGAAA‑AAAAAATTTCTCCTTTCTGAGTGGTCCCCTTCTCCCTATTTTTTCA‑CGCCGCA‑TTCTTTAGGGGACg                                                                                               >  1:18591/1‑150 (MQ=255)                                                     ttCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAAGAAA‑AACGATTTTCTCCTTTTTGAGTGCTCCCCCTCTCCCTCTTATTTCA‑CCCAGGA‑TTTTTTAg                                                                                                     >  1:578119/1‑144 (MQ=255)                                                       ctctGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTTAGGACA‑TAAAAATTTCTCCTTTTTAATTGCTCCGCTTCTCACTATTATCTCA‑CCCAAGA‑TTTTTAAAGGGACGa                                                                                              >  1:480113/1‑149 (MQ=255)                                                       ctctGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTTAAGAAA‑TAAGATTTTCTCCTTTTTGAGTGGTCCGCCTCTCCCTATTATTTCC‑CCCAGTA‑TTTTTAAaggga                                                                                                 >  1:749879/1‑144 (MQ=255)                                                                    tGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGGCAATAATA‑TAAAACTTTCTCCTTTCCTAGAGGTGCGCTTCTCCCCATTCTCTCA‑CCCACAC‑TTTTTTAATGAAAGATAAAGA‑GGaaacccg                                                                              >  2:429646/1‑146 (MQ=255)                                                                       ataatGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTTAGGAAA‑AAAAATTTTCTCCTTTCTTAAGGTTGCGCTTCTCCCCTTTAAATCA‑CATCGCA‑TTCTTAAGGGAAAGATaaaaggggaacatgaa                                                                             >  2:762775/1‑136 (MQ=255)                                                                        taatGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTATTTACATTACAATTT‑CTTCTTTCTTAGGGGGCCGCCTCTCCCTATTATTTTC‑CTCCGTC‑TTCTTTTTGGGAAGATAAAGA‑GGCAACATGa                                                                             >  2:624926/1‑148 (MQ=255)                                                                          atGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAAGAAA‑AAAAATTTTCTCCCTTCTTAGTGCCCCGCCTCTCACTATTTTTTCACCCCCGAT‑TTTTTAAGGGAA‑GATAAAGA‑GGaaaccagaaaa                                                                          >  1:684405/1‑140 (MQ=255)                                                                                aTCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACA‑TACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCA‑CGCAGTA‑TTCTTAAGGGAACGATAAGGA‑GGAACCATGAACATTAcccc                                                                   <  2:362155/150‑1 (MQ=255)                                                                                     cAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACA‑TACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCA‑CGCAGTA‑TTCTTAAGGGAACGATAAGGA‑GGAACCATGAACATTACCCCGTTTcc                                                             <  1:364475/151‑1 (MQ=255)                                                                                         aTTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGGTAAAGAAA‑AAAGATTTTCTCCTTTTTGAGGGCTCCCCTTCTCTCTATTTTTTCA‑CCCAGTA‑TTTTTTTGGGAACGAAAAAGAGGGAACCTTAAACTTTACCCC‑TTTCCgcc                                                          >  1:181505/1‑148 (MQ=255)                                                                                          tttCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTTATGAAA‑TAAGATTTTCTTCTTTCTGAGTGGTCCGCTTCTCACTCTTATTTCA‑CACCGGA‑TTTTTTAAGGAAAGATAAAGA‑GGAAACAAGAAACATACCCCCTTTTCGAc                                                          >  2:626686/1‑149 (MQ=255)                                                                                             ccTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTTAAGAAA‑TAAGATTTTCTCCCTTTATAGTGGTCCCCCTCTCCCTATTTTTTTA‑CGCAGTATTTTTTAAGGGAA‑GAAAAAGA‑GGAAACATTAACATTAACCCCCTTTCGACGCctt                                                     >  1:717936/1‑151 (MQ=255)                                                                                                tAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACA‑TACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCA‑CGCAGTA‑TTCTTAAGGGAACGATAAGGA‑GGAACCATGAACATTACCCCGTTTCCGACGCTTTc                                                    <  1:332452/149‑1 (MQ=255)                                                                                                tAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACA‑TACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCA‑CGCAGTA‑TTCTTAAGGGAACGATAAGGA‑GGAACCATGAACATTACCCCGTTTCCGACGCTTTCg                                                   <  2:665698/150‑1 (MQ=255)                                                                                                    aGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACA‑TACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCA‑CGCAGTA‑TTCTTAAGGGAACGATAAGGA‑GGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGc                                              <  1:230846/151‑1 (MQ=255)                                                                                                      atatGTCAGGCTTGCGGAGTGGCGGTTAAGGACA‑TACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCA‑CGCAGTA‑TTCTTAAGGGAACGATAAGGA‑GGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCaa                                            <  1:415026/151‑1 (MQ=255)                                                                                                      atatGTCAGGCTTGCGGAGTGGCGGTTAAGGACA‑TACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCA‑CGCAGTA‑TTCTTAAGGGAACGATAAGGA‑GGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCaa                                            <  1:655915/151‑1 (MQ=255)                                                                                                        atGTCAGGCTTGCGGAGTGGCGGTTAAGGACA‑TACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCA‑CGCAGTA‑TTCTTAAGGGAACGATAAGGA‑GGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACt                                          <  1:410558/151‑1 (MQ=255)                                                                                                          gTCAGGCTTGCGGAGTGGCGGTTAAGGACA‑TACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCA‑CGCAGTA‑TTCTTAAGGGAACGATAAGGA‑GGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACtat                                        <  2:749518/151‑1 (MQ=255)                                                                                                                         tGGCGGTTAAGGACA‑TACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCA‑CGCAGTA‑TTCTTAAGGGAACGATAAGGA‑GGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGAAGCCATAAAt                           >  2:755154/1‑149 (MQ=255)                                                                                                                              gTTAAGGACA‑TACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCA‑CGCAGTA‑TTCTTAAGGGAACGATAAGGA‑GGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCg                    >  2:156948/1‑151 (MQ=255)                                                                                                                                 aaGGACA‑TACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCA‑CGCAGTA‑TTCTTAAGGGAACGATAAGGA‑GGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGa                  <  1:315158/150‑1 (MQ=255)                                                                                                                                     aCA‑TACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCA‑CGCAGTA‑TTCTTAAGGGAACGATAAGGA‑GGAACCATGATCATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGACAGtg             <  2:548515/151‑1 (MQ=255)                                                                                                                                      cA‑TACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCA‑CGCAGTA‑TTCTTAAGGGAACGATAAGGA‑GGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGACAGtgg            <  1:764738/151‑1 (MQ=255)                                                                                                                                                 cctcctTTCAGAGTGCTCCGCTTCTCACTATTATCTCA‑CGCAGTA‑TTCTTAAGGGAACGATAAGGA‑GGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGACAGTGGCTGGCGCAgg  >  1:654364/1‑151 (MQ=255)                                                                                                                                                 |                                                                                                                                                          TATTAATTCTAAAACGGTAAGGGTAAAAATTCAGGAATTCAGAAAAATACAATTCTCTGCTGCAAGATGAATAATGTTTATCTACAGCATTTCCTTAAAAGATATGTCAGGCTTGCGGAGTGGCGGTTAAGGACA‑TACGATTTCCTCCTTTCAGAGTGCTCCGCTTCTCACTATTATCTCA‑CGCAGTA‑TTCTTAAGGGAACGATAAGGA‑GGAACCATGAACATTACCCCGTTTCCGACGCTTTCGCCGGCAACTATAGATGCCATAAATGTTATCGGACAGTGGCTGGCGCAGG  >  NC_000913/1487020‑1487313

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑