Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	2,425,968	T→G	12.1%	intergenic (‑52/+38)	hisQ ← / ← hisJ	lysine/arginine/ornithine ABC transporter/histidine ABC transporter, membrane subunit HisQ/histidine ABC transporter periplasmic binding protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,425,968	0	T	G	12.1%	99.6 / 4.0	48	intergenic (‑52/+38)	hisQ/hisJ	lysine/arginine/ornithine ABC transporter/histidine ABC transporter, membrane subunit HisQ/histidine ABC transporter periplasmic binding protein
Reads supporting (aligned to +/- strand):  ref base T (25/16);  new base G (4/3);  total (29/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.11e-01

CGATGATTACAGCGAGCACTACAGAGCTGATAGCCAGCTCCAGCGTGACGAGCGCACCCTGTAAAATAACACCTGAAAACCCATACAACATGCTGCCTGTCCTGTCGTGTGT‑GGTGAATTACCGCCTCTTGTCTCCCTCCGGTTACCCGAAGGGAGCGGGCTTTCTTTCACCGATGGCGATTAG‑CCACCATAAACATCAAAATCGAAGTACTTTTTCGCTAATTTCTCGTAAGTACCGTCAGCGCGCATTTCGGCAAAGGCTTTGTTCAGTGCTTCGCGCAGTTC  >  NC_000913/2425826‑2426110                                                                                                                                                |                                                                                                                                                cGATGATTACAGCGAGCACTACAGAGCTGATAGCCAGCTCCAGCGTGACGAGCGCACCCTGTAAAATAACACCTGAACCTACATTCAACATGCTGCCCGTCCATTTGGGTGT‑GGTGAATTACCGCCTCTTGTCTCCCTCCGGt                                                                                                                                                 >  1:601558/1‑143 (MQ=255)    tgatTACAGCGAGCACTACAGAGCTGATAGCCAGCTCCAGCGTGACGAGCGCACCCTGTAAAATAACACCTGAAAACCCATACAACATGCTGCCTGTCCTGTCGTGTGT‑GGTGAATTACCGCCTCTTGTCTCCCTCCGGTTAc                                                                                                                                              >  1:465849/1‑143 (MQ=255)           agccggCACTACAGAGCTGAGAGCCAGCTCCAGCGTGACGCGCGCACCCTGTAAAATAACACCTGACAACCCATACAACACGCTGCCTGTCCTGTCCTGTGT‑GGTGAATTACCGCCTCTTGTCTCCCTCCGGTTACCCGAAgg                                                                                                                                       <  1:139457/138‑1 (MQ=255)                       agagCTGATAGCCAGCTCCAGCGTGACGAGCGCACCCTGTAAAATAACACCTGAAAACCCATACACCATGCTGCCTGTCCTGTCGTGTGT‑GGTGAATTACCGCCTCTTGTCTCCCTCCGGTTACCCCAGGGGTGCGGGctttc                                                                                                                           >  1:86240/1‑143 (MQ=255)                        gcgCTGATAGCCAGCTCCAGCGTGACGAGCGCACCCTGTAAAATAACACCTGAAAACCCATACAACATGCTGCCTGTCCTGTCGTGTGT‑GGTGAATTACCGCCTCTTGTCTCCCTCCGGTTACCCGAAGGGAGCGGGctttct                                                                                                                          <  1:548883/141‑1 (MQ=255)                          ggcggtAGCCAGCGCCAGCGGGACGAGCGCACCCTGTAAAATAACACCTGAAAACCCATACAACATGCTGCCTGTCCTGTCGTGTGT‑GGTGAATTACCGCCTCTTGTCTCCCTCCGGTTACCCGAAGGGAGCGGGctttcttt                                                                                                                        <  2:371300/138‑1 (MQ=255)                            tGATAGCCAGCTCCAGCGTGACGAGCGCACCCTGTAAAATAACACCTGAAAACCCATACAACATGCTGCCTGTCCTGTCGTGTGT‑GGTGAATTACCGCCTCTTGTCTCCCTCCGGTTACCCGAAGGGAGCGGGCTTTCTTTCa                                                                                                                      >  1:8361/1‑143 (MQ=255)                             gagaGCCAGCGCCAGCGTGACGAGCGCACCCTGTCAAATTACGCCTGAAAACCCATACAACCTGCTGCCTGTCCTGTCGTGTGT‑GGTGAATTACCGCCTCTTGTCTCCCTCCGGGTACCCGAAGGGAGCGGGCTTTCTTTCAc                                                                                                                     <  2:251295/140‑1 (MQ=255)                              aTAGCCAGCTCCAGCGTGACGAGCGCACCCTGTAAAATAACACCTGAAAACCCATACAACATGCTGCCTGTCCTGTCGTGTGT‑GGTGAATTACCGCCTCTTGTCTCCCTCCGGTTACCCGAAGGGAGCGGGCTTTCTTTCAcc                                                                                                                    >  2:668118/1‑143 (MQ=255)                                      ctgcAGCGTGACGAGCGCACCCTGTAAAATAACACCTGAAAACCCATACAACATGCTGCCTGTCCTGTCGTGTGT‑GGTGAATTACCGCCTCTTGTCTCCCTCCGGTTACCCGAAGGGAGCGGGCTTTCTTTCACCGATGGCgc                                                                                                            >  2:646206/4‑142 (MQ=255)                                      cTCCAGCGTGACGAGCGCACCCTGTAAAATAACACCGAAACACCCATACAACATGCTGCCTGTCCTGTCGTGTGT‑GACGAAGTGCGGCCTCTTGTCTCGCGCCGGGTGCGCGAAGGCAGCGGGCTGGCGTTGACCGGTGGCGa                                                                                                            >  2:444845/1‑143 (MQ=255)                                        ccAGCGTGACGAGCGCACCCTGTAAAATAACACCTGAAAACCCATACAACATGCTGCCTGTCCTGTCGTGTGT‑GGTGAATTACCGCCTCTTGTCTCCCTCCGGTTACCCGAAGGGAGCGGGCTTTCTTTCACCGACGGCGAtt                                                                                                          >  1:372553/1‑143 (MQ=255)                                         cAGCGTGACGAGCGCACCCTGTAAAATAACACCTGAAAACCCATACAACATGCTGCCTGTCCTGTCGTGTGT‑GGTGAATTACCGCCTCTTGTCTCCCTCCGGTTACCCGAAGGGAGCGGGCTTTCTTTCACCGATGGCGATTa                                                                                                         >  1:412106/1‑143 (MQ=255)                                                aCGAGCGCACCCTGTAAAATAACACCTGAAAACCCATACAACATGCTGCCTGTCCTGTCGTGTGT‑GGTGAATTACCGCCTCTTGTCTCCCTCCGGTTACCCGACGGGAGCGGGCTTTCTTTCACCGCTGGCGATTAG‑ccacca                                                                                                 >  2:449482/1‑143 (MQ=255)                                                       cgcccTGTAAAATAACACCTGAAAACCCATACAACATGCTGCCTGTCCTGTCGTGTGT‑GGTGAATTACCGCCTCTTGTCTCCCTCCGGTTACCCGAAGGGAGCGGGCTTTCTTTCACCGATGGCGATTAG‑CCACCATAAACAt                                                                                          <  1:663424/141‑1 (MQ=255)                                                            tGTAAAATAACACCTGAAAACCCATACAACATGCTGCCTGTCCTGTCGTGTGT‑GGTGAATTACCGCCTCTTGTCTCCCTCCGGTTACCCGAAGGGAGCGGGCTTTCTTTCACCGACGGCGATTAG‑CCCCCACAAACATCcaaa                                                                                     >  2:148309/1‑143 (MQ=255)                                                                gattAACACCTGAAACCCCAGACAACAGCCTGCCGGTCCGGTCGTGTGT‑GGTGAATTACCGCCTCTTGTCTCCCGCCGGTTACCCGAAGGGAGCGGGCTTTCTTTCACCGATGGCGATTAG‑CCATCATAAACATCAAAATCGa                                                                                 <  2:180682/140‑1 (MQ=255)                                                                  aTAACACCTGAAAACCCATACAACATGCTGCCTGTCCTGTCGTGTGT‑GGTGAATTACCGCCTCTTGTCTCCCTCCGGTTACCCGCAGGGAGCGGGCTTTCTTTCACCGATGGCGATTAG‑CCACCATAAACATCAAAATCGAAg                                                                               >  2:287725/1‑143 (MQ=255)                                                                           gAAAACCCATACAACATGCTGCCTGTCCTGTCGTGTGT‑GGTGAATTACCGCCTCTTGTCTCCCTCCGGTTACCCGAAGGGAGCGGGCTTTCTTTCACCGATGGCGATTAG‑CCACCATAAACATCAAAATCGAAGTACTTTTTc                                                                      <  1:668118/143‑1 (MQ=255)                                                                           gAAAACCCAAACAACAGGCGGCCTGTCCGGGCGGGTGT‑GGTGAATTACCGCCTCTTGTCTCCCTCCGGGTACCCGAAGGGAGCGGGCTTTCTTTCACCGATGGCGATTAG‑CCACCATAAACATCAAAATCGAAGTACTTTTTc                                                                      <  1:281665/143‑1 (MQ=255)                                                                                  cATACAACATGCTGTCTGTCCTGTCGTGTGT‑GGTGAATTACCGCCTCTTGTCTCCCTCCGGTTACCCGAAGGGAGCGGGCTTTCTTTCACCGATGGCGATTAG‑CCACCATAAACATCAAAATCGAAGTACTTTTTCGCTAAtt                                                               <  1:55327/143‑1 (MQ=255)                                                                                   aTACAACATGCTGCCTGTCCTGTCGTGTGT‑GGTGAATTACCGCCTCTTGTCTCCCTCCGGTTACCCGAAGGGAGCGGGCTTTCTTTCACCGGTGGCGCTTAG‑CCACCATAAACATGAAACTCGACGTACTTTTTCGCTAAgtt                                                              >  1:170922/1‑143 (MQ=255)                                                                                      caacaTGCTGCCTGTCCTGTCGTGTGT‑GGTGAATTACCGCCTCTTGTCTCCCTCCGGTTACCCGAAGGGAGCGGGCTTTGTTTCACCGCTGGCGATTGGTCGACCA‑AAACATCAAAATCGAAGTACTTTTTCGCTAATTtctc                                                           >  2:293822/1‑143 (MQ=255)                                                                                       aaccTGCGGCCTGTCCTGTCGTGTGT‑GGTGAAGTACCGCCTCTTGTCTCCCTCCGGTTACCCGAAGGGAGCGGGCTTTCTTTCACCGATGGCGATTAG‑CCACCATAAACATCAAAATCGAAGTACTTTTTCGCTAATTTCTCg                                                          <  2:592242/143‑1 (MQ=255)                                                                                         cttgctgcCTGTCCTGTCGTGTGT‑GGTGAATTACCGCCTCTTGTCTCCCTCCGGTTACCCGAAGGGAGCGGGCTTTCTTTCACCGATGGCGATTAG‑CCACCATAAACATCAAAATCGAAGTACTTTTTCGCTAATTTCTCGTa                                                        <  2:216778/141‑1 (MQ=255)                                                                                          gtgctggCTGTCCGGTCGTGTGT‑GGTGGATTACCGCCTCTTGTCTCCCTCCGGTTACCCGAAGGGAGCGGGCTTTCTTTCACCGATGGCGATTAG‑CCACCATAAACATCAAAATCGAAGTACTTTTTCGCTAATTTCTCGTaa                                                       <  2:509837/142‑1 (MQ=255)                                                                                          aTGCTGCCTGTCCTGTCGTGTGT‑GGTGAATTACCGCCTCTTGTCTCCCTCCGGGTACCCGAAGGGAGCGGGCTTTCTTTCACCGATGGCGATTAG‑CCACCATAAACATCAAAATCGAAGTACTTTTTCGCTAATTTCTCGTaa                                                       <  2:195482/143‑1 (MQ=255)                                                                                            gctgcCTGTCCTGTCGTGTGT‑GGTGAATTACCGCCTCTTGTCTCCCTCCGGTTACCCGAAGGGAGCGGGCTTTCTTTCACCGATGGCGATTAG‑CCACCATAAACATCAAAATCGAAGTACTTTTTCGCTAATTTCTCGTAAGt                                                     <  2:601558/143‑1 (MQ=255)                                                                                              tgcCTGTCCTGTCGTGTGT‑GATGATTCTCCTCCTCTGGTCTCCCTCCGGTTACCCGAAGGGTGCGGGCTGTCTTTCACCGATGGCGATTAG‑CCACCATAAACATCAACATCGAAGTACTTTTTCGCTCATTTCTCCTAAGtcc                                                   >  2:238810/1‑141 (MQ=255)                                                                                                      ctgtcGTGTGT‑GGTGAATTACCGCCTCTTGTCTCCCTCCGGTTACCCGAAGGGAGCGGGCTTTCTTTCACCGATGGCGATTAG‑CCACCATAAACATCAAAATCGAAGTACTTTTTCGCTAATTTCTCGTAAGTACCGTCAgcg                                           >  1:68819/1‑143 (MQ=255)                                                                                                      ctgtcGTGTGT‑GGTGAATTACCGCCTCTTGTCTCACTCCGGTTACCCGAAGGGAGCGGGCTTTCTTTCACCGATGGCGATTAG‑CCACCATAAACATCAAAATCGAAGTACTCTTTCGATCATTTGTCGTACGTACCGTccacg                                           >  2:149873/1‑139 (MQ=255)                                                                                                       tgtcGTGTGTCGGTG‑ACTGCTGCGTCTTCTCGCCCGCCTGTTACCCGAAGGGAGCTGGCTTTCTTTCCCCGATGGCGATTAG‑CCACCATAAACATCAAAATCGAAGTACTTTGTCGCTAATTTCTCGTAAGTACCGTCAgcgc                                          <  2:104620/143‑1 (MQ=255)                                                                                                        gtcGTGTGT‑GGTGAATTACCGCCTCTTGTCTCCCTCCGGTTACCCGAAGGGAGCGGGCTTTCTTTCACCGATGGCGATTAG‑CCACCATAAACATCAAAATCGAAGTACTTTTTCGCTAATTTCTCGTAAGTACCGTCAgcgcg                                         >  1:370288/1‑143 (MQ=255)                                                                                                         tcGTGTGT‑GGTGAATTACTGCCTCTTGTCTCCCTCCGGTTACCCGAAGGGAGCGGGCTTTCTTGCACCGATGGCGCTTAG‑CCACCATAAACATCAAAATCGAAGGACTTCTTCGCTAATGTCTCGTACGTACCATCAgcgcgc                                        >  2:410032/1‑143 (MQ=255)                                                                                                           gtgtgt‑GGTGAATTACCGCCTCTTGTCTCCCTCCGGTTACCCGAAGGGAGCGGGCTTTCTTTCACCGATGGCGATTAG‑CCACCATAAACATCAAAATCGAAGTACTTTTTCGCTAATTTCTCGTAAGTACCGTCAGCGCGCAt                                      >  1:113719/1‑143 (MQ=255)                                                                                                            tgtgt‑gGTGAATTACCGCCTCTTGTCTCCCTCCGGTTACCCGAAGGGAGCGGGCTTTCTTTCACCGATGGCGATTAG‑CCACCATAAACATCAAAATCAACGCACTTCCCAGCTGTTTGCTCGTAAGTACCGTCAGCGCGCAtt                                     >  1:635692/1‑143 (MQ=255)                                                                                                                t‑ggtgAATTACCGCCTCTTGTCTCCCTCCGGTTACCCGAAGGGAGCGGGCTTTCTTTCACCGATGGCGATTAG‑CCACCATAAACATCAAAATCGAAGTACTTTTTCGCTCATTTCCCGTACGTACCGTCCGCGCGCACTTCgc                                 >  1:287535/1‑142 (MQ=255)                                                                                                                   gtgAATTACCGCCTCTTGTCTCCCTCCGGTTACCCGAAGGGAGCGGGCTTTCTTTCACCGATGGCGATTAG‑CCACCATAAACATCAAAATCGAAGTACTTTTTCGCTAATTTCTCGTAAGTACCGTCAGCGCGCATTTCGGCa                               >  2:499203/1‑143 (MQ=255)                                                                                                                    tgAATTACCGCCTCTTGTCTCCCTCCGGTTACCCGAAGGGAGCGGGCTTTCTTTCACCGATGGCGATTAG‑CCACCATAAACATCAAAATCGAAGTACTTTTTCGCTAATTTCTCGTAAATACCGTCAACACGCATTTCGGCaa                              >  2:672297/1‑143 (MQ=255)                                                                                                                        ttACCGCCTCTTGTCTCCCTCCGGTTACCCGAAGGGAGCGGGCTTTCTTTCACCGATGGCGATTAG‑CCACCATAAACATCAAAATCGAAGTACTTTTTCGCTAATTTCTCGTAAGTACCGTCAGCGCGGATTTCGGCAAAGGc                          >  1:631730/1‑143 (MQ=255)                                                                                                                         tACCGCCTCTTGTCTCCCTCCGGTTACCCCAAGGAAGTCGGTTTTCTTTCACCGATGGCGATTAG‑CCACCATAAACATCAAAATCGAAGTACTTTTTCGCTAATTTCTCGTAAGTACCGTCAGCGCGCATTTCGGCAAAGGCt                         <  1:22996/143‑1 (MQ=255)                                                                                                                            cGCCTCTTGTCTCCCTCCGGTTACCCGAAGGGAGCGGGCTGTCTTTCACCGATGGCGATTAG‑CCACCATAAACATCAAAATCGAAGTACTTTTTCGCTAATTTCTCGTAAGTACCGTCAGCGCGCATTTCGGCAAAGGCTTTg                      >  2:480039/1‑143 (MQ=255)                                                                                                                                    cgctcccttcGGGTAACCGGAGGGAGCGGGCTTTCTTTCACCGATGGCGATTAG‑CCACCATAAACATCAAAATCGAAGTACTTTTTCGCTAATTTCTCGTCAGTACCGTCAGCGCGCATTTCGGCCAAGGCTTTGTTCAGTGc              >  2:274357/3‑143 (MQ=255)                                                                                                                                    cgctcccttcGGGTAACCGGAGGGAGCGGGCTTTCTTTCACCGATGGCGATTAG‑CCACCATAAACATCAAAATCGAAGTACTTTGTCGCTAATTTCTCGTAAGTACCGTCAGCGCGCATTTCGGCAAAGGCTTTGTTCAGTGc              >  1:204769/3‑143 (MQ=255)                                                                                                                                      ctcccttcGGGTAACCGGAGGGAGCGGGCTTTCTTTCACCGATGGCGGTTAG‑CCACCATAAACATCAAAATCGCAGTACTTTTTCGCTAATTTCTCGTAGCTACCTTCAGCGCGCCTTTCGGCAAAGACTTTTTTCAGTGCtt            >  1:419973/1‑143 (MQ=255)                                                                                                                                      ctccctccGGTTACCGGATGGGAGCGGGCTTTCTTTCACCGATGGCGATTAG‑CCACCATAAACATCAAAATCGAAGTACTTTGTCGCTAATTTCTCGTAAGTACCGTCAGCGCGCATTTCGGCAAAGGCTTTGTTCAGTGCtt            <  2:249402/143‑1 (MQ=255)                                                                                                                                          ctccGGTGACCCGAAGGGAGCGGGCTTTCGTTCACCGATGGCGATTAG‑CCACCATAAACATCAAAATCGAAGTACTTTTTCGCTAATTTCTCGTAAGTACCGTCAGCGCGCATTTCGGCAAAGGCTTTGTTCAGTGCTTcgcg        <  2:618363/143‑1 (MQ=255)                                                                                                                                            ccGGTTACCCGAAGGGAGCGGGCTTTCTTTCACCGATGGCGATTAG‑CCACCATAAACATCAAAATCGAAGTACTTTTTCGCTAATTTCTCGTAAGTACCGTCAGCGCGCATTTCGGCAAAGGCTTTGTTCAGTGCTTCGCGCa      <  1:169440/143‑1 (MQ=255)                                                                                                                                             cGGTTACCCGAAGGGAGCGGGCTTTCTTTCACCGATGGCGATTAG‑CCACCATAAACATCACACTCGAAGTACTTTTTCGCTAATTTCTCGTAAGTACCGTCAGCGCGCATTTCGGCAAAGGCTTTGTTCAGGGCTTCgcgcgg     >  2:491804/1‑141 (MQ=255)                                                                                                                                                ttACCCGAAGGGAGCGGGCTTTCTTTCACCGATGGCGATTAG‑CCACCATAAACATCAAAATCGAAGTACTTTTTCGCTAATTTCTCGTAAGTACCGTCAGCGCGCATTTCGGCAAAGGCTTTGTTCAGTGCTTCGCGCAGTTc  <  1:495706/143‑1 (MQ=255)                                                                                                                                                |                                                                                                                                                CGATGATTACAGCGAGCACTACAGAGCTGATAGCCAGCTCCAGCGTGACGAGCGCACCCTGTAAAATAACACCTGAAAACCCATACAACATGCTGCCTGTCCTGTCGTGTGT‑GGTGAATTACCGCCTCTTGTCTCCCTCCGGTTACCCGAAGGGAGCGGGCTTTCTTTCACCGATGGCGATTAG‑CCACCATAAACATCAAAATCGAAGTACTTTTTCGCTAATTTCTCGTAAGTACCGTCAGCGCGCATTTCGGCAAAGGCTTTGTTCAGTGCTTCGCGCAGTTC  >  NC_000913/2425826‑2426110

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑