Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	987,494	0	T	G	47.8%	65.0 / 10.8	46	intergenic (‑512/+91)	ompF/asnS	outer membrane porin 1a (Ia;b;F)/asparaginyl tRNA synthetase
Reads supporting (aligned to +/- strand):  ref base T (2/22);  new base G (22/0);  total (24/22)
Fisher's exact test for biased strand distribution p-value = 3.51e-11
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TCAGACATCCAGAATGCCAAAAAATAGTATGAAAATTGTGCTATTAGCTAAGAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGTTGC‑AAATAGA‑TTGCTTGACTTAACAAACAGAT‑AACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAATTAGAAGCTGGCGTTACGCGGAGTACGTGGGAACGGAATCACATCACGTACGTT  >  NC_000913/987350‑987638                                                                                                                                                 |                                                                                                                                                    tCAGACATCCAGAATGCCAAAAAATAGTATGAAAATTGTGCTATTAGCTAAGAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGTTGC‑aa                                                                                                                                               <  1:154703/150‑1 (MQ=255)   aGACATCCAGAATGCCAAAAAATAGTATGAAAATTGTGCTATTAGCTAAGAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGTTGC‑AAATa                                                                                                                                            <  1:450925/151‑1 (MQ=255)   aGACATCCAGAATGCCAAAAAATAGTATGAAAATTGTGCTATTAGCTAAGAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGGTGG‑aaa                                                                                                                                              >  1:493872/1‑149 (MQ=255)    gACATCCAGAATGCCAAAAAATAGTATGAAAATTGTGCTATTAGCTAAGAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGGTGG‑GAATa                                                                                                                                            >  2:466730/1‑150 (MQ=255)       aTCCAGAATGCCAAAAAATAGTATGAAAATTGTGCTATTAGCTAAGAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGGTGG‑AAATa                                                                                                                                            >  1:657873/1‑147 (MQ=255)       aTCCAGAATGCCAAAAAATAGTATGAAAATTGTGCTATTAGCTAAGAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGGTGC‑aa                                                                                                                                               >  2:286125/1‑144 (MQ=255)           aGAATGCCAAAAAATAGTATGAAAATTGTGCTATTAGCTAAGAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGGTGC‑TAAAAAA‑ATGCtt                                                                                                                                   >  2:404872/1‑151 (MQ=255)               tGCCAAAAAATAGTATGAAAATTGTGCTATTAGCTAAGAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGGTGC‑CAAAAGA‑TTGttt                                                                                                                                   >  2:550667/1‑147 (MQ=255)                gCCAAAAAATAGTATGAAAATTGTGCTATTAGCTAAGAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGTTGC‑AAATAGA‑TTGCTTGACtt                                                                                                                              <  1:623526/151‑1 (MQ=255)                     aaaaTAGTATGAAAATTGTGCTATTAGCTAAGAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGGTGT‑AAAAAGA‑TTGATTGTCTTtaca                                                                                                                          >  1:567771/1‑150 (MQ=255)                      aaaTAGTATGAAAATTGTGCTATTAGCTAAGAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGTTGC‑AAATAGA‑TTGCTTGACTTaacaaa                                                                                                                        <  1:586450/151‑1 (MQ=255)                       aaTAGTATGAAAATTGTGCTATTAGCTAAGAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGTTGC‑AAATAGA‑TTGCTTGACTTaacaaac                                                                                                                       <  1:385231/151‑1 (MQ=255)                            tATGAAAATTGTGCTATTAGCTAAGAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGGTGG‑AAATAGA‑TTTTTTGTCTTaaaaaaaaaa                                                                                                                    >  2:532043/1‑145 (MQ=255)                                  aaTTGTGCTATTAGCTAAGAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGTTGC‑AAATAGA‑TTGCTTGACTTAACAAACAGAT‑AACTTGa                                                                                                           <  1:23154/151‑1 (MQ=255)                                    ttGTGCTATTAGCTAAGAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGGTGG‑AAATAAA‑ATTCTTGACTTtacaaacaaaaaaatt                                                                                                              >  2:617914/1‑139 (MQ=255)                                     tgtgCTATTAGCTAAGAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGTTGC‑AAATAGA‑TTGCTTGACTTAACAAACAGAT‑AACTTGACa                                                                                                         <  2:109983/150‑1 (MQ=255)                                        gCTATTAGCTAAGAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGTTGC‑AAATAGA‑TTGCTTGACTTAACAAACAGAT‑AACTTGACAGaaa                                                                                                     <  1:714919/151‑1 (MQ=255)                                        gCTATTAGCTAAGAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGGTGCGAAAAAAA‑TTG‑TTGACTTAAAAAAAAAAA‑AAATTGACAGaa                                                                                                      >  2:495599/1‑150 (MQ=255)                                           aTTAGCTAAGAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGGTGC‑AAATAGA‑ATGTTTTACTTAAAAAAAAAAA‑AAACTTACAGaaaa                                                                                                    >  2:39225/1‑149 (MQ=255)                                                   aGAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGTTGC‑AAATAGA‑TTGCTTGACTTAACAAACAGAT‑AACTTGACAGAAAAGATaaaaaaa                                                                                          <  2:156928/151‑1 (MQ=255)                                                   aGAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGGTGC‑AAAAAGATTTGTTTGA‑TTAACAAAAAGAT‑AAATTTAGAGAAAAGATaaaaaa                                                                                           >  2:462106/1‑150 (MQ=255)                                                    gAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGTTGC‑AAATAGA‑TTGCTTGACTTAACAAACAGAT‑AACTTGACAGAAAAGATAAAAAAag                                                                                         <  2:721973/151‑1 (MQ=255)                                                      aaaaaCTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGTTGC‑AAATAGA‑TTGCTTGACTTAACAAACAGAT‑AACTTGACAGAAAAGATAAAAAAagag                                                                                       <  1:65396/151‑1 (MQ=255)                                                       aaaaCTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGTTGC‑AAAAAAA‑TTTCTTTACTTAAAAAACAAAT‑AACTTGGCAGaaaaaaaaaaaaaaa                                                                                         >  1:565708/1‑147 (MQ=255)                                                            tAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGGTGG‑AAATAAA‑TTTCTTGACTTTACAAAAAGAA‑AACTTTACAGAAAAGATaaaaaaaaaaac                                                                                     >  2:56098/1‑142 (MQ=255)                                                                 cGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGGCGT‑CAATAGA‑ATTGTTTAGTTACCAGAAACAC‑AAACTGGCCCAAAAGATaaaaaaaaaaaaacggggg                                                                              >  2:500536/1‑137 (MQ=255)                                                                   cAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGTTGC‑AAATAGA‑TTGCTTGACTTAACAAACAGAT‑AACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTg                                                                          <  1:233001/151‑1 (MQ=255)                                                                   cAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGGTGC‑AAATAGA‑TTTGTTTAATTTAAAAAAAAAA‑AAATTTACAGAAAAAAAAAAAAAAAAAACAGCggggg                                                                             >  2:404197/1‑146 (MQ=255)                                                                        aGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGTTGC‑AAATAGA‑TTGCTTGACTTAACAAACAGAT‑AACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGctct                                                                     <  2:8865/151‑1 (MQ=255)                                                                         gAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGTTGC‑AAATAGA‑TTGCTTGACTTAACAAACAGAT‑AACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCtt                                                                    <  2:308084/151‑1 (MQ=255)                                                                          aaTGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGTTGC‑AAATAGA‑TTGCTTGACTTAACAAACAGAT‑AACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTg                                                                   <  2:54015/151‑1 (MQ=255)                                                                                      tttttGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGGTGG‑AAAAAAA‑ATGTTTTACTTAACAAAAAAAA‑AAATTTTCAGAAAAAAAAAAAAAAAAAACAACGGGGGGTGGGCCTTTAAAAAGCTaaa                                                        >  1:295520/1‑150 (MQ=255)                                                                                       ttttGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGCGGTGG‑AAATAAA‑TTGCTTGAGTTTATAAAAAAATAAAATTCAC‑GAAAAAATAAAAAAAAAACCAACCGGCGGCGGCCCTTgcaaaagcgaaa                                                        >  1:646806/1‑138 (MQ=255)                                                                                            cgcgTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGGTGG‑AAAAAAA‑TTTCTTTAATTTACAAAAAAAA‑AAATTGACAAAAAAAAAAAAAAAAAAAACAGCGGGGGCCGGGTCTTTGAAAAGCTAAAtt                                                      >  1:635422/1‑146 (MQ=255)                                                                                                tAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGGTGG‑AAATAAA‑TTGTTTTTCTTTACAAAAAAAA‑AAATTGACAGAAAAAAAAAAAAAAAAACCAACGGGGGCCGGGCCTTTAAGACGCtaaaataaaaaat                                               >  2:47321/1‑146 (MQ=255)                                                                                                     gTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGGTGG‑AAAAAAA‑ATTGTTTTCTTTAAAAAAAGAA‑AAATTGACAGAAAAAATAAAAAAAAAAACAACGGGCGCTAGCGCTTTAAAAAGCTAAATTaaaaaattgcg                                           >  1:678168/1‑141 (MQ=255)                                                                                                           aTGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGTTGC‑AAATAGA‑TTGCTTGACTTAACAAACAGAT‑AACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAATTAGAAGCTGGCGTTACGCGGa                                  <  1:686835/151‑1 (MQ=255)                                                                                                            tGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGGTGG‑AAAAAAA‑ATTCTTTGCTTTAAAAAAAAAA‑AAATTTACAGAAAAAAAAAAAAAAAAAACAACGGGGGCTGGGTCTTTGAGAAGCTAAAATAAAAAAAGGCGGTTCGCgg                                   >  2:618880/1‑149 (MQ=255)                                                                                                               aaTATTCCGTAACAGGATGATCGTTATGGCGGGGTTGC‑AAATAGA‑TTGCTTGACTTAACAAACAGAT‑AACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAATTAGAAGCTGGCGTTACGCGGAGTAc                              <  1:495473/151‑1 (MQ=255)                                                                                                                       gTAACAGGATGATCGTTATGGCGGGGGTGG‑AAAAAAA‑TTGTTTGTCTTTAAAAAAAAAT‑AAATTTACAGAAAAAAAAAAAAAAAAACCAGCGGGGGCCGGCGCTTTTAGAAGCTAAAATAAAAACTGGCGGTACGCGGAGTACGgggg                         >  2:138349/1‑148 (MQ=255)                                                                                                                          aCAGGATGATCGTTATGGCGGGGTTGC‑AAATAGA‑TTGCTTGACTTAACAAACAGAT‑AACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAATTAGAAGCTGGCGTTACGCGGAGTACGTGGGAACGGa                   <  2:333095/151‑1 (MQ=255)                                                                                                                             ggATGATCGTTATGGCGGGGTTGC‑AAATAGA‑TTGCTTGACTTAACAAACAGAT‑AACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAATTAGAAGCTGGCGTTACGCGGAGTACGTGGGAACGGAatc                <  1:710955/151‑1 (MQ=255)                                                                                                                                  atCGTTATGGCGGGGTTGC‑AAATAGA‑TTGCTTGACTTAACAAACAGAT‑AACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAATTAGAAGCTGGCGTTACGCGGAGTACGTGGGAACGGAatcacata           <  1:444119/151‑2 (MQ=255)                                                                                                                                    cGTTATGGCGGGGTTGC‑AAATAGA‑TTGCTTGACTTAACAAACAGAT‑AACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAATTAGAAGCTGGCGTTACGCGGAGTACGTGGGAACGGAatcacatcac         <  1:227464/151‑1 (MQ=255)                                                                                                                                           gCGGGGTTGC‑AAATAGA‑TTGCTTGACTTAACAAACAGAT‑AACTTGACAGAGAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAATTAGAAGCTGGCGTTACGCGGAGTACGTGGGAACGGAATCACATCACGTACGtt  <  1:649437/151‑1 (MQ=255)                                                                                                                                           gCGGGGTTGC‑AAATAGA‑TTGCTTGACTTAACAAACAGAT‑AACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAATTAGAAGCTGGCGTTACGCGGAGTACGTGGGAACGGAATCACATCACGTACGtt  >  1:730868/1‑151 (MQ=255)                                                                                                                                                 |                                                                                                                                                    TCAGACATCCAGAATGCCAAAAAATAGTATGAAAATTGTGCTATTAGCTAAGAAAAAACTAATCCGCAATAAGAATGCGGATTAGTTTTTGCGCGTAAATGTTGCAATGTAATATTCCGTAACAGGATGATCGTTATGGCGGGGTTGC‑AAATAGA‑TTGCTTGACTTAACAAACAGAT‑AACTTGACAGAAAAGATAAAAAAAGAGCCAGCGGGCGCTGGCTCTTGAAGACGCTAAATTAGAAGCTGGCGTTACGCGGAGTACGTGGGAACGGAATCACATCACGTACGTT  >  NC_000913/987350‑987638

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑