Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,641,812	A→G	intergenic (‑258/‑43)	cspB ← / → cspF	Qin prophage; cold shock‑like protein CspB/Qin prophage; cold shock protein CspF

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,641,812	0	A	G	100.0%	177.9 / NA	48	intergenic (‑258/‑43)	cspB/cspF	Qin prophage; cold shock‑like protein CspB/Qin prophage; cold shock protein CspF
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (27/21);  total (27/21)

GTAAACTACTTCGTATATCGTCTGTTCTTCAAACCGACGCAATCATTAACGCATAGTTGAACATATGAAGCAATGTTTATTTTAGACATCCAGCCATCTTCAACCCCATCAAAAAACTATAGCTTTCTTCAGGAACGTGTGTATAGTGCGCCAAGTTATCAGTATTAAGGAATTTTTTTGTCCCGTAAAATGACAGGAATTGTCAAAACCTTTGACGGCAAAAGCGGCAAGGGTCTTATCACCCCATCCGATGGTCGTATCG  >  NC_000913/1641678‑1641939                                                                                                                                       |                                                                                                                                gTAAACTACTTCGTATATCGTCTGTTCTTCAAACCGACGCAATCATTAACGCATAGTTGAACATATGAAGCAATGTTTATTTTAGACATCCAGCCATCTTCAACCCCATCAAAAAACTATAGCTTTCTTCAGGAGCgtgt                                                                                                                            >  1:663268/1‑140 (MQ=255)         ctTCGTATATCGTCTGTTCTTCAAACCGACGCAATCATTAACGCATAGTTGAACATATGAAGCAATGTTTATTTTAGACATCCAGCCATCTTCAACCCCATCAAAAAACTATAGCTTTCTTCAGGAGCGTGTGTATAGTg                                                                                                                    >  1:449252/1‑140 (MQ=255)            cGTATATCGTCTGTTCTTCAAACCGACGCAATCATTAACGCATAGTTGAACATATGAAGCAATGTTTATTTTAGACATCCAGCCATCTTCAACCCCATCAAAAAACTATAGCTTTCTTCAGGAGCGTGTGTATAGTgcgc                                                                                                                 >  1:388188/1‑140 (MQ=255)                    gTCTGTTCTTCAAACCGACGCAATCATTAACGCATAGTTGAACATATGAAGCAATGTTTATTTTAGACATCCAGCCATCTTCAACCCCATCAAAAAACTATAGCTTTCTTCAGGAGCGTGTGTATAGTGCGCCAAGTTAt                                                                                                         >  1:954634/1‑140 (MQ=255)                     tCTGTTCTTCAAACCGACGCAATCATTAACGCATAGTTGAACATATGAAGCAATGTTTATTTTAGACATCCAGCCATCTTCAACCCCATCAAAAAACTATAGCTTTCTTCAGGAGCGTGTGTATAGTGCGcc                                                                                                                >  2:385384/1‑132 (MQ=255)                     tCTGTTCTTCAAACCGACGCAATCATTAACGCATAGTTGAACATATGAAGCAATGTTTATTTTAGACATCCAGCCATCTTCAACCCCATCAAAAAACTATAGCTTTCTTCAGGAGCGTGTGTATAGTGCGcc                                                                                                                <  1:385384/132‑1 (MQ=255)                      cTGTTCTTCAAACCGACGCAATCATTAACGCATAGTTGAACATATGAAGCAATGTTTATTTTAGACATCCAGCCATCTTCAACCCCATCAAAAAACTATAGCTTTCTTCAGGAGCGTGTGTATAGTGCGCCAAGTTATCa                                                                                                       >  1:816596/1‑140 (MQ=255)                           cttcAAACCGACGCAATCATTAACGCATAGTTGAACATATGAAGCAATGTTTATTTTAGACATCCAGCCATCTTCAACCCCATCAAAAAACTATAGCTTTCTTCAGGAGCGTGTGTATAGTGCGCCAAg                                                                                                             <  2:396969/129‑1 (MQ=255)                           cttcAAACCGACGCAATCATTAACGCATAGTTGAACATATGAAGCAATGTTTATTTTAGACATCCAGCCATCTTCAACCCCATCAAAAAACTATAGCTTTCTTCAGGAGCGTGTGTATAGTGCGCCAAg                                                                                                             >  1:396969/1‑129 (MQ=255)                                           tCATTAACGCATAGTTGAACATATGAAGCAATGTTTATTTTAGACATCCAGCCATCTTCAACCCCATCAAAAAACTATAGCTTTCTTCAGGAGCGTGTGTATAGTGCGCCAAGTTATCAGTATTAAGGAATTTTTTTGTc                                                                                  >  1:438061/1‑140 (MQ=255)                                                 aCGCATAGTTGAACATATGAAGCAATGTTTATTTTAGACATCCAGCCATCTTCAACCCCATCAAAAAACTATAGCTTTCTTCAGGAGCGTGTGTATAGTGCGCCAAGTTATCAGTATTAAGGAATTTTTTTGTCCCGTaa                                                                            <  1:362151/140‑1 (MQ=255)                                                    cATAGTTGAACATATGAAGCAATGTTTATTTTAGACATCCAGCCATCTTCAACCCCATCAAAAAACTATAGCTTTCTTCAGGAGCGTGTGTATAGTGCGCCAAGTTATCAGTATTAAGGAATTTTTTTGTCCCGTAAAAt                                                                         >  1:1027142/1‑140 (MQ=255)                                                     aTAGTTGAACATATGAAGCAATGTTTATTTTAGACATCCAGCCATCTTCAACCCCATCAAAAAACTATAGCTTTCTTCAGGAGCGTGTGTATAGTGCGCCAAGTTATCAGTATTAAGGAATTTTTTTGTCCCGTAAAATg                                                                        >  2:611214/1‑140 (MQ=255)                                                     aTAGTTGAACATATGAAGCAATGTTTATTTTAGACATCCAGCCATCTTCAACCCCATCAAAAAACTATAGCTTTCTTCAGGAGCGTGTGTATAGTGCGCCAAGTTATCAGTATTAAGGAATTTTTTTGTCCCGTAAAATg                                                                        >  2:60119/1‑140 (MQ=255)                                                      tAGTTGAACATATGAAGCAATGTTTATTTTAGACATCCAGCCATCTTCAACCCCATCAAAAAACTATAGCTTTCTTCAGGAGCGTGTGTATAGTGCGCCAAGTTATCAGTATTAAGGAATTTTTTTGTCCCGTAAAATGa                                                                       <  2:449252/140‑1 (MQ=255)                                                            aaCATATGAAGCAATGTTTATTTTAGACATCCAGCCATCTTCAACCCCATCAAAAAACTATAGCTTTCTTCAGGAGCGTGTGTATAGTGCGCCAAGTTATCAGTATTAAGGAATTTTTTTGTCCCGTAAAATGACAGGaa                                                                 <  2:954634/140‑1 (MQ=255)                                                             aCATATGAAGCAATGTTTATTTTAGACATCCAGCCATCTTCAACCCCATCAAAAAACTATAGCTTTCTTCAGGAGCGTGTGTATAGTGCGCCAAGTTATCAGTATTAAGGAATTTTTTTGTCCCGTAAAATGACAGGAAt                                                                >  2:551948/1‑140 (MQ=255)                                                                 atGAAGCAATGTTTATTTTAGACATCCAGCCATCTTCAACCCCATCAAAAAACTATAGCTTTCTTCAGGAGCGTGTGTATAGTGCGCCAAGTTATCAGTATTAAGGAATTTTTTTGTCCCGTAAAATGACAGGAATTGTc                                                            >  2:880623/1‑140 (MQ=255)                                                                 atGAAGCAATGTTTATTTTAGACATCCAGCCATCTTCAACCCCATCAAAAAACTATAGCTTTCTTCAGGAGCGTGTGTATAGTGCGCCAAGTTATCAGTATTAAGGAATTTTTTTGTCCCGTAAAATGACAGGAATTGTc                                                            >  1:300739/1‑140 (MQ=255)                                                                   gAAGCAATGTTTATTTTAGACATCCAGCCATCTTCAACCCCATCAAAAAACTATAGCTTTCTTCAGGAGCGTGTGTATAGTGCGCCAAGTTATCAGTATTAAGGAATTTTTTTGTCCCGTAAAATGACAGGAATTGTCaa                                                          >  1:378955/1‑140 (MQ=255)                                                                   gAAGCAATGTTTATTTTAGACATCCAGCCATCTTCAACCCCATCAAAAAACTATAGCTTTCTTCAGGAGCGTGTGTATAGTGCGCCAAGTTATCAGTATTAAGGAATTTTTTTGTCCCGTAAAATGACAGGAATTGTCaa                                                          >  1:1148880/1‑140 (MQ=255)                                                                         aTGTTTATTTTAGACATCCAGCCATCTTCAACCCCATCAAAAAACTATAGCTTTCTTCAGGAGCGTGTGTATAGTGCGCCAAGTTATCAGTATTAAGGAATTTTTTTGTCCCGTAAAATGACAGGAATTGTCAAAACCtt                                                    >  1:739912/1‑140 (MQ=255)                                                                         aTGTTTATTTTAGACATCCAGCCATCTTCAACCCCATCAAAAAACTATAGCTTTCTTCAGGAGCGTGTGTATAGTGCGCCAAGTTATCAGTATTAAGGAATTTTTTTGTCCCGTAAAATGACAGGAATTGTCAAAACCtt                                                    >  1:992911/1‑140 (MQ=255)                                                                           gTTTATTTTAGACATCCAGCCATCTTCAACCCCATCAAAAAACTATAGCTTTCTTCAGGAGCGTGTGTATAGTGCGCCAAGTTATCAGTATTAAGGAATTTTTTTGTCCCGTAAAATGACAGGAATTGTCAAAACCTTTg                                                  >  1:297231/1‑140 (MQ=255)                                                                           gTTTATTTTAGACATCCAGCCATCTTCAACCCCATCAAAAAACTATAGCTTTCTTCAGGAGCGTGTGTATAGTGCGCCAAGTTATCAGTATTAAGGAATTTTTTTGTCCCGTAAAATGACAGGAATTGTCAAAACCTTTg                                                  >  2:263875/1‑140 (MQ=255)                                                                                   tAGACATCCAGCCATCTTCAACCCCATCAAAAAACTATAGCTTTCTTCAGGAGCGTGTGTATAGTGCGCCAAGTTATCAGTATTAAGGAATTTTTTTGTCCCGTAAAATGACAGGAATTGTCAAAACCTTTGACGGCaaa                                          <  1:263875/140‑1 (MQ=255)                                                                                         tCCAGCCATCTTCAACCCCATCAAAAAACTATAGCTTTCTTCAGGAGCGTGTGTATAGTGCGCCAAGTTATCAGTATTAAGGAATTTTTTTGTCCCGTAAAATGACAGGAATTGTCAAAACCTTTGACGGCAAAAGCGGc                                    <  2:1148880/140‑1 (MQ=255)                                                                                         tCCAGCCATCTTCAACCCCATCAAAAAACTATAGCTTTCTTCAGGAGCGTGTGTATAGTGCGCCAAGTTATCAGTATTAAGGAATTTTTTTGTCCCGTAAAATGACAGGAATTGTCAAAACCTTTGACGGCAAAAGCGGc                                    <  2:1088078/140‑1 (MQ=255)                                                                                          ccAGCCATCTTCAACCCCATCAAAAAACTATAGCTTTCTTCAGGAGCGTGTGTATAGTGCGCCAAGTTATCAGTATTAAGGAATTTTTTTGTCCCGTAAAATGACAGGAATTGTCAAAACCTTTGACGGCAAAAGCGGCa                                   <  1:270140/140‑1 (MQ=255)                                                                                          ccAGCCATCTTCAACCCCATCAAAAAACTATAGCTTTCTTCAGGAGCGTGTGTATAGTGCGCCAAGTTATCAGTATTAAGGAATTTTTTTGTCCCGTAAAATGACAGGAATTGTCAAAACCTTTGACGGCAAAAGCGGCa                                   <  2:300739/140‑1 (MQ=255)                                                                                          ccAGCCATCTTCAACCCCATCAAAAAACTATAGCTTTCTTCAGGAGCGTGTGTATAGTGCGCCAAGTTATCAGTATTAAGGAATTTTTTTGTCCCGTAAAATGACAGGAATTGTCAAAACCTTTGACGGCAAAAGCGGCa                                   >  2:889589/1‑140 (MQ=255)                                                                                          ccAGCCATCTTCAACCCCATCAAAAAACTATAGCTTTCTTCAGGAGCGTGTGTATAGTGCGCCAAGTTATCAGTATTAAGGAATTTTTTTGTCCCGTAAAATGACAGGAATTGTCAAAACCTTTGACGGCAAAAGCGGCa                                   <  1:551948/140‑1 (MQ=255)                                                                                             gCCATCTTCAACCCCATCAAAAAACTATAGCTTTCTTCAGGAGCGTGTGTATAGTGCGCCAAGTTATCAGTATTAAGGAATTTTTTTGTCCCGTAAAATGACAGGAATTGTCAAAACCTTTGACGGCAAAAGCGGCAAgg                                <  1:880623/140‑1 (MQ=255)                                                                                             gCCATCTTCAACCCCATCAAAAAACTATAGCTTTCTTCAGGAGCGTGTGTATAGTGCGCCAAGTTATCAGTATTAAGGAATTTTTTTGTCCCGTAAAATGACAGGAATTGTCAAAACCCTTGACGGCAAAAGCGGCAAgg                                <  2:816596/140‑1 (MQ=255)                                                                                              ccATCTTCAACCCCATCAAAAAACTATAGCTTTCTTCAGGAGCGTGTGTATAGTGCGCCAAGTTATCAGTATTAAGGAATTTTTTTGTCCCGTAAAATGACAGGAATTGTCAAAACCTTTGACGGCAAAAGCGGCAAggg                               <  1:723094/140‑1 (MQ=255)                                                                                                   ttCAACCCCATCAAAAAACTATAGCTTTCTTCAGGAGCGTGTGTATAGTGCGCCAAGTTATCAGTATTAAGGAATTTTTTTGTCCCGTAAAATGACAGGAATTGTCAAAACCTTTGACGGCAAAAGCGGCAAGGGTCTTa                          >  1:767620/1‑140 (MQ=255)                                                                                                     cAACCCCATCAAAAAACTATAGCTTTCTTCAGGAGCGTGTGTATAGTGCGCCAAGTTATCAGTATTAAGGAATTTTTTTGTCCCGTAAAATGACAGGAATTGTCAAAACCTTTGACGGCAAAAGCGGCAAGGGTCTTATc                        >  1:571824/1‑140 (MQ=255)                                                                                                        ccccATCAAAAAACTATAGCTTTCTTCAGGAGCGTGTGTATAGTGCGCCAAGTTATCAGTATTAAGGAATTTTTTTGTCCCGTAAAATGACAGGAATTGTCAAAACCTTTGACGGCAAAAGCGGCAAGGGTCTTATCAcc                     >  1:185206/1‑140 (MQ=255)                                                                                                           cATCAAAAAACTATAGCTTTCTTCAGGAGCGTGTGTATAGTGCGCCAAGTTATCAGTATTAAGGAATTTTTTTGTCCCGTAAAATGACAGGAATTGTCAAAACCTTTGACGGCAAAAGCGGCAAGGGTCTTATCACCCCa                  >  1:415167/1‑140 (MQ=255)                                                                                                            aTCAAAAAACTATAGCTTTCTTCAGGAGCGTGTGTATAGTGCGCCAAGTTATCAGTATTAAGGAATTTTTTTGTCCCGTAAAATGACAGGAATTGTCAAAACCTTTGACGGCAAAAGCGGCAAGGGTCTTATCACCCCAt                 >  2:457473/1‑140 (MQ=255)                                                                                                            aTCAAAAAACTATAGCTTTCTTCAGGAGCGTGTGTATAGTGCGCCAAGTTATCAGTATTAAGGAATTTTTTTGTCCCGTAAAATGACAGGAATTGTCAAAACCTTTGACGGCAAAAGCGGCAAGGGTCTTATCACCCCAt                 >  1:1094707/1‑140 (MQ=255)                                                                                                                aaaaaCTATAGCTTTCTTCAGGAGCGTGTGTATAGTGCGCCAAGTTATCAGTATTAAGGAATTTTTTTGTCCCGTAATATGACAGGAATTGTCAAACCCTTTGACGGCAAAAGCGGCAAGGGTCTTATCGCCCCATCCGa             <  2:1027142/140‑1 (MQ=255)                                                                                                                aaaaaCTATAGCTTTCTTCAGGAGCGTGTGTATAGTGCGCCAAGTTATCAGTATTAAGGAATTTTTTTGTCCCGTAAAATGACAGGAATTGTCAAAACCTTTGACGGCAAAAGCGGCAAGGGTCTTATCACCCCATCCGa             <  2:388188/140‑1 (MQ=255)                                                                                                                aaaaaCTATAGCTTTCTTCAGGAGCGTGTGTATAGTGCGCCAAGTTATCAGTATTAAGGAATTTTTTTGTCCCGTAAAATGACAGGAATTGTCAAAACCTTTGACGGCAAAAGCGGCAAGGGTCTTATCACCCCATCCGa             <  2:378955/140‑1 (MQ=255)                                                                                                                          gCTTTCTTCAGGAGCGTGTGTATAGTGCGCCAAGTTATCAGTATTAAGGAATTTTTTTGTCCCGTAAAATGACAGGAATTGTCAAAACCTTTGACGGCAAAAGCGGCAAGGGTCTTATCACCCCATCCGATGGTCGTATc   <  1:889589/140‑1 (MQ=255)                                                                                                                           cTTTCTTCAGGAGCGTGTGTATAGTGCGCCAAGTTATCAGTATTAAGGAATTTTTTTGTCCCGTAAAATGACAGGAATTGTCAAAACCTTTGACGGCAAAAGCGGCAAGGGTCTTATCACCCCATCCGATGGTCGTATCg  <  2:438061/140‑1 (MQ=255)                                                                                                                           cTTTCTTCAGGAGCGTGTGTATAGTGCGCCAAGTTATCAGTATTAAGGAATTTTTTTGTCCCGTAAAATGACAGGAATTGTCAAAACCTTTGACGGCAAAAGCGGCAAGGGTCTTATCACCCCATCCGATGGTCGTATCg  <  1:611214/140‑1 (MQ=255)                                                                                                                           cTTTCTTCAGGAGCGTGTGTATAGTGCGCCAAGTTATCAGTATTAAGGAATTTTTTTGTCCCGTAAAATGACAGGAATTGTCAAAACCTTTGACGGCAAAAGCGGCAAGGGTCTTATCACCCCATCCGATGGTCGTATCg  <  1:60119/140‑1 (MQ=255)                                                                                                                                       |                                                                                                                                GTAAACTACTTCGTATATCGTCTGTTCTTCAAACCGACGCAATCATTAACGCATAGTTGAACATATGAAGCAATGTTTATTTTAGACATCCAGCCATCTTCAACCCCATCAAAAAACTATAGCTTTCTTCAGGAACGTGTGTATAGTGCGCCAAGTTATCAGTATTAAGGAATTTTTTTGTCCCGTAAAATGACAGGAATTGTCAAAACCTTTGACGGCAAAAGCGGCAAGGGTCTTATCACCCCATCCGATGGTCGTATCG  >  NC_000913/1641678‑1641939

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑