Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,736,784	0	T	C	42.1%	52.5 / 12.0	38	G169G (GGA→GGG)	ydhP	putative MFS transporter, inner membrane protein
Reads supporting (aligned to +/- strand):  ref base T (16/6);  new base C (0/16);  total (16/22)
Fisher's exact test for biased strand distribution p-value = 4.62e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GTAAACATTGCACCAGCTCCCAGTACCGTCGTCAGCAATGCAGACAGCACCTGCGGACGCATTAATACCGCCAGCTCTTTTTTCACTTCAGGTCGTGCCCCTGCACCACCTTTAGGTAATGAGAAGAACAGACTTACC‑ATTG‑AAAT‑CACTCCCAG‑CCCCGCCGTTGCCAGAAATGACATCCGCCAGCCGATGGTTTCACCCAACCAGGTCGCCGCCGGCACGCCACCGATATTTGCCAGGGTTAACCCCATAAACATAGTGGCAACTGCGCTGGCCTGTTTATGTTTTGGCACCACGCTT  >  NC_000913/1736635‑1736934                                                                                                                                                         |                                                                                                                                                        gTAAACATTGCACCAGCTCCCAGTACCGTCGTCAGCAATGCAGACAGCACCTGCGGACGCATTAATACCGCCAGCTCTTTTTTCACTTCAGGTCGTGCCCCTGCACCACCTTTAGGTAATGAGAAGAACAGACTTACC‑ATTG‑AAAT‑CACTc                                                                                                                                                        <  1:198111/151‑1 (MQ=255)    aaCATTGCACCAGCTCCCAGTACCGTCGTCAGCAATGCAGACAGCACCTGCGGACGCATTAATACCGCCAGCTCTTTTTTCACTTCAGGTCGTGCCCCTGCACCACCTTTAGGTAATGAGAAGAACAGACTTACC‑ATTG‑AAAT‑CACTccc                                                                                                                                                      >  1:355513/1‑150 (MQ=255)    aaCATTGCACCAGCTCCCAGTACCGTCGTCAGCAATGCAGACAGCACCTGCGGACGCATTAATACCGCCAGCTCTTTTTTCACTTCAGGTCGTGCCCCTGCACCACCTTTAGGTAATGAGAAGAACAGACTTACC‑ATTG‑AAAT‑CACTCCCa                                                                                                                                                     <  1:911308/151‑1 (MQ=255)    aaCATTGCACCAGCTCCCAGTACCGTCGTCAGCAATGCAGACAGCACCTGCGGACGCATTAATACCGCCAGCTCGTTTTTCACTTCAGGTCGTGCACCTGCACCACCTTTAGGTAATGAGAAGAACAGACTTACC‑ATTG‑AAAT‑CACTCCCa                                                                                                                                                     <  2:586877/151‑1 (MQ=255)     aCATTGCACCAGCTCCCAGTACCGTCGTCAGCAATGCAGACAGCACCTGCGGACGCATTAATACCGCCAGCTCTTTTTTCACTTCAGGTCGTGCCCCTGCACCACCTTTAGGTAATGAGAAGAACAGACTTACC‑ATTG‑AAAT‑CACTCCCAg                                                                                                                                                    <  2:623772/151‑1 (MQ=255)          gCACCAGCTCCCAGTACCGTCGTCAGCAATGCAGACAGCACCTGCGGACGCATTAATACCGCCAGCTCTTTTTTCACTTCAGGTCGTGCCCCTGCACCACCTTTAGGTAATGAGAAGAACAGACTTACC‑ATTG‑AAAT‑CACTCCCAG‑CCccg                                                                                                                                              <  1:147988/151‑1 (MQ=255)               aGCTCCCAGTACCGTCGTCAGCAATGCAGACAGCACCTGCGGACGCATTAATACCGCCAGCTCTTTTTTCACTTCAGGTCGTGCCCCTGCACCACCTTTAGGTAATGAGAAGAACAGACTTACC‑ATTG‑AAAT‑CACTCCCAG‑CCCCGCCGtt                                                                                                                                         >  2:457195/1‑151 (MQ=255)               aGCTCCCAGTACCGTCGTCAGCAATGCAGACAGCACCTGCGGACGCATTAATACCGCCAGCTCTTTTTTCACTTCAGGTCGTGCCCCTGCACCACCTTTAGGTAATGAGAAGAACAGACTTACC‑ATTG‑AAAT‑CACTCCCAG‑CCCCGCCGtt                                                                                                                                         >  1:530466/1‑151 (MQ=255)                           cgtcgtCAGCAATGCAGACAGCACCTGCGGACGCATTAATACCGCCAGCTCTTTTTTCACTTCAGGTCGTGCCCCTGCACCACCTTTAGGTAATGAGAAGAACAGACTTACC‑ATTG‑AAAT‑CACTCCCAG‑CCCCGCCGTTGCCAGAAATGAc                                                                                                                             >  1:837370/1‑151 (MQ=255)                                     aatgaaaacacacccTGGGGACGTATTAATACCGCCAGCTCTTTTTTCACTTCGGGTCGTCCCCCGGCCCCCCTTTTGTTTAAGGAAAAAAACAGATTTCCC‑ATTA‑AAAC‑CCCCCCCAG‑CCCCGCCGTTGCCAGAAATGACATCCGCCa                                                                                                                     <  1:576454/136‑1 (MQ=255)                                     aaggCAGACAGCCCCTGGGGACCAATAAATCCCGCCAGCTTTTTTTTCACTTCAGGTCGTCCCCCTGCACCCCCTTTAGGTAATGAGAAGAACAGACTTCCC‑ATTA‑AAAT‑CCCTCCCAG‑CCCCGCCGTTGCCAGAAATGACATCCGCCa                                                                                                                     <  1:272197/146‑1 (MQ=255)                                     aaTGCAGACACCCCCTGCGGACGCATAAATCCCGCCAGCTTTTTTTTCACTTCAGGTCGGGCCCCTGCCCCCCCTTTAGGTAATGAAAAGAACAGACTTACC‑ATTG‑AAAC‑CCCCCCCAG‑CCCCGCCGTTGCCAGAAATGACATCCGcc                                                                                                                      <  1:251892/148‑1 (MQ=255)                                                              ttAATCCCGCCAGCTTTTTTTTCACTTCAGTTCGTCCCCCTCCCCCCCCTTTAGGTAATGAGAAAAACAGCCTTCCC‑ATTA‑AAAC‑CCCCCCCGG‑CCCCGCCGTTGCCAGAAATGACATCCGCCAGCCGATGGTTTCACCCAACCAGGTcg                                                                                           <  1:303012/150‑1 (MQ=255)                                                                aaccccGCCATCTTTTTTTTCCCTTCAGGTCGCCCCCCCCCCCCACCTTTAGGTAATAAAAAAAACAGACTTACC‑TTTA‑AAAC‑CCCCCCCCC‑CCCCGCCGTTGCCAGAAATGACATCCGCCAGCCGATGGTTTCACCCAACCAGGTcgccg                                                                                        <  2:80439/147‑1 (MQ=255)                                                                   aCCGCCAGCTCTTTTTTCACTTCAGGTCGTGCCCCTGCACCACCTTTAGGTAATGAGAAGAACAGACTTACC‑ATTG‑AAAT‑CACTCCCAG‑CCCCGCCGTTGCCAGAAATGACATCCGCCAGCCGATGGTTTCACCCAACCAGGTCGccgccg                                                                                     >  1:39113/1‑151 (MQ=255)                                                                    ccccgaGCTTTTTTTTCCCTAAAGGCCGGCCCCCTCACCCCCCTTAAGGTAAGAAAAAAAACAGAC‑TACC‑TTTA‑AAATCCTCCCCAAG‑CCCCGCCGTTGCCAGAAATGACATCCGCCAGCCGATGGTTTCACCCAACCAGGTCgccgcc                                                                                      <  2:383104/144‑1 (MQ=255)                                                                    ccGCCACCTTTTTTTTCACTCCAGGTCGTCCCCCTGCCCCCCTTTTAGGTAAGGAAAAAAACAGA‑TTTCC‑ATTGAAAAT‑CCCCCCCAG‑CCCCGCCGTTGCCAGAAATGACATCCGCCAGCCGATGGTTTCACCCAACCAGGTCgccgcc                                                                                      <  1:339119/149‑1 (MQ=255)                                                                           ctctTTTTTCACTTCAGGTCGTGCCCCTGCACCACCTTTAGGTAATGAGAAGAACAGACTTACC‑ATTG‑AAAT‑CACTCCCAG‑CCCCGCCGTTGCCAGAAATGACATCCGCCAGCCGATGGTTTCACCCAACCAGGTCGCCGCCGGCACGcc                                                                              >  2:366629/1‑150 (MQ=255)                                                                              ttttttCACTACAGGTCGTCCCCCTCCCCCCCTTTTAGGAAATGAAAAAAACAGCCTTCCC‑ATTA‑AAAC‑CCCCCCCAC‑CCCCGCCGTTGCCAGAAATGACATCCGCCAGCCGATGGTTTCACCCAACCAGGTCGCCGCCGGCACGCCAcc                                                                           <  1:149889/150‑1 (MQ=255)                                                                                tttacccTTCAGGCCGCCCCCCTCCCCCCCCTTAAGGTAATGAAAAAAACAG‑CTTCCC‑CATG‑AAAA‑CCCCCCCCGCCCCCGCCGTTGCCAGAAATGACATCCGCCAGCCGATGGTTTCACCCAACCAGGTCGCCGCCGGCACGCCACCGa                                                                         <  2:864389/144‑1 (MQ=255)                                                                                   tCACTTCAGGTCGTGCCCCTGCACCACCTTTAGGTAATGAGAAGAACAGACTTACC‑ATTG‑AAAT‑CACTCCCAG‑CCCCGCCGTTGCCAGAAATGACATCCGCCAGCCGATGGTTTCACCCAACCAGGTCGCCGCCGGCACGCCACCGATAtt                                                                     >  2:419101/1‑151 (MQ=255)                                                                                     aCTTCAGGTCGTGCCCCTGCACCACCTTTAGGTAATGAGAAGAACAGACTTACC‑ATTG‑AAAT‑CACTCCCAG‑CCCCGCCGTTGCCAGAAATGACATCCGCCAGCCGATGGTTTCACCCAACCAGGTCGCCGCCGGCACGCCACCGATATTTg                                                                   >  2:427891/1‑151 (MQ=255)                                                                                       tacggttCGTCCCCCTCCCCCCCTTTAAGGTAATGAAAAAAAAATA‑TTACCTTTTG‑AAAT‑CCCCCCCAC‑CCCCGCCGTTGCCAGAAATGACATCCGCCAGCCGATGGTTTCACCCAACCAGGTCGCCGCCGGCACGCCACCGATAtt                                                                     <  2:259829/141‑1 (MQ=255)                                                                                            gTCGTGCCCCTGCACCACCTTTAGGTAATGAGAAGAACAGACATACC‑ATTG‑AAAT‑CACTCCCAG‑CCCCGCCGTTGCCAGAAATGACATCCGCCAGCCGATGGTTTCACCCAACCAGGTCGCCGCCGGCACGCCACCGATATTTGCCAGGGt                                                            >  1:512812/1‑151 (MQ=255)                                                                                              cGTGCCCCTGCACCACCTTTAGGTAATGAGAAGAACAGACTTACC‑ATTG‑AAAT‑CACTCCCAG‑CCCCGCCGTTGCCAGAAATGACATCCGCCAGCCGATGGTTTCACCCAACCAGGTCGCCGCCGGCACGCCACCGATATTTGCCAGGGtt                                                           >  1:349407/1‑150 (MQ=255)                                                                                                       ccccccccTTAAGGTAAGGAAAAGAACAGACTTACC‑ATTA‑AAAC‑CCCCCCCAC‑CCCCGCCGTTGCCAGAAATGACATCCGCCAGCCGATGGTTTCACCCAACCAGGTCGCCGCCGGCACGCCACCGATATTTGCCAGGGTTAACCCCATa                                                  <  1:633492/144‑1 (MQ=255)                                                                                                        ccccccttttAGGTAATGAGAAAAACAGACTTCCC‑ATGA‑AAAT‑CCCCCCCAG‑CCCCGCCGTTGCCAGAAATGACATCCGCCAGCCGATGGTTTCACCCAACCAGGTCGCCGCCGGCACGCCACCGATATTTGCCAGGGTTAACCCCATa                                                  <  1:801345/142‑1 (MQ=255)                                                                                                              cTTTAGGTAATGAGAAGAACAGACTTACC‑ATTG‑AAAT‑CACTCCCAG‑CCCCGCCGTTGCCAGAAATGACATCCGCCAGCCGATGGTTTCACCCAACCAGGTCGCCGCCGGCACGCCACCGATATTTGCCAGGGTTAACCCCATAAACATAGt                                          >  2:453013/1‑151 (MQ=255)                                                                                                                    gTAATGAGAAGAACAGACTTACC‑ATTG‑AAAT‑CACTCCCAG‑CCCCGCCGTTGCCAGAAATGACATCCGCCAGCCGATGGTTTCACCCAACCAGGTCGCCGCCGGCACGCCACCGATATTTGCCAGGGTTAACCCCATAAACATAGTGGCAAc                                    >  2:911723/1‑151 (MQ=255)                                                                                                                      aaTGAGAAGAACAGACTTACC‑ATTG‑AAAT‑CACTCCCAG‑CCCCGCCGTTGCCAGAAATGACATCCGCCAGCCGATGGTTTCACCCAACCAGGTCGCCGCCGGCACGCCACCGATATTTGCCAGGGTTAACCCCATAAACATAGTGGCAACTg                                  >  1:255660/1‑151 (MQ=255)                                                                                                                        ggaaaaaaaCAGCCTTCCC‑ATAA‑AAAT‑CCCCCCCCG‑CCCCGCCGTTGCCAGAAATGACATCCGCCAGCCGATGGTTTCACCCAACCAGGTCGCCGCCGGCACGCCACCGATATTTGCCAGGGTTAACCCCATAAACATAGTGGCAACTgc                                 <  2:19385/143‑1 (MQ=255)                                                                                                                            aagaaAAGACTTCCA‑ATTA‑AAAC‑CCCCCCCAC‑CCCCGCCGTTGCCAGAAATGACATCCGCCAGCCGATGGTTTCACCCAACCAGGTCGCCGCCGGCACGCCACCGATATTTGCCAGGGTTAACCCCATAAACATAGTGGCAACTGCGCTgg                            <  2:259699/151‑1 (MQ=255)                                                                                                                               aaCAGATTTACA‑ATTA‑AAAC‑CCCCCCCAC‑CCCCGCCGTTGCCAGAAATGACATCCGCCAGCCGATGGTTTCACCCAACCAGGTCGCCGCCGGCACGCCACCGATATTTGCCAGGGTTAACCCCATAAACATAGTGGCAACTGCGCTGGCCt                         <  1:151878/151‑1 (MQ=255)                                                                                                                               aaCAGACTTACC‑ATTG‑AAAT‑CACTCCCAG‑CCCCGCCGTTGCCAGAAATGACATCCGCCAGCCGATGGTTTCACCCAACCAGGTCGCCGCCGGCACGCCACCGATATTTGCCAGGGTTAACCCCATAAACATAGTGGCAACTGCGCTGGCCt                         >  1:391930/1‑151 (MQ=255)                                                                                                                                      ttccc‑ATTG‑AAAT‑CCCCCCCAC‑CCCCGCCGTTGCCAGAAATGACATCCGCCAGCCGATGGTTTCACCCAACCAGGTCGCCGCCGGCACGCCACCGATATTTGCCAGGGTTAACCCCATAAACATAGTGGCAACTGCGCTGGCCTGttt                     <  1:715486/145‑1 (MQ=255)                                                                                                                                      ttACC‑ATTA‑AAAC‑CCCCCCCAC‑CCCCGCCGTTGCCAGAAATGACATCCGCCAGCCGATGGTTTCACCCAACCAGGTCGCCGCCGGCACGCCACCGATATTTGCCAGGGTTAACCCCATAAACATAGTGGCAACTGCGCTGGCCTGTTTAt                   <  1:815966/150‑1 (MQ=255)                                                                                                                                             ttG‑AAAT‑CACTCCCAG‑CCCCGCCGTTGCCAGAAATGACATCCGCCAGCCGATGGTTTCACCCAACCAGGTCGCCGCCGGCACGCCACCGATATTTGCCAGGGTTAACCCCATAAACATAGTGGCAACTGCGCTGGCCTGTTTATGTTTTgg            >  1:721784/1‑151 (MQ=255)                                                                                                                                             ttG‑AAAT‑CACTCCCAG‑CCCCGCCGTTGCCAGAAATGACATCCGCCAGCCGATGGTTTCACCCAACCAGGTCGCCGCCGGCACGCCACCGATATTTGCCAGGGTTAACCCCATAAACATAGTGGCAACTGCGCTGGCCTGTTTATGTTTTgg            >  2:632726/1‑151 (MQ=255)                                                                                                                                                         tCCCAG‑CCCCGCCGTTGCCAGAAATGACATCCGCCAGCCGATGGTTTCACCCAACCAGGTCGCCGCCGGCACGCCACCGATATTTGCCAGGGTTAACCCCATAAACATAGTGGCAACTGCGCTGGCCTGTTTATGTTTTGGCACCACGCtt  >  1:153534/1‑151 (MQ=255)                                                                                                                                                         |                                                                                                                                                        GTAAACATTGCACCAGCTCCCAGTACCGTCGTCAGCAATGCAGACAGCACCTGCGGACGCATTAATACCGCCAGCTCTTTTTTCACTTCAGGTCGTGCCCCTGCACCACCTTTAGGTAATGAGAAGAACAGACTTACC‑ATTG‑AAAT‑CACTCCCAG‑CCCCGCCGTTGCCAGAAATGACATCCGCCAGCCGATGGTTTCACCCAACCAGGTCGCCGCCGGCACGCCACCGATATTTGCCAGGGTTAACCCCATAAACATAGTGGCAACTGCGCTGGCCTGTTTATGTTTTGGCACCACGCTT  >  NC_000913/1736635‑1736934

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑