Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,569,309	G→A	pseudogene (312/921 nt)	yjiP →	pseudogene, transposase_31 family protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,569,309	0	G	A	100.0%	127.5 / NA	40	pseudogene (312/921 nt)	yjiP	pseudogene, transposase_31 family protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (23/17);  total (23/17)

CGCTACACTCCGATATTTTATGGTCGGTAAAGACCCGCGAAGGCGATGGCTATATCTATGTGGTGATTGAACATCAGAGCCGCGAGGACATTCATATGGCCTTTCGCCTGATGCGCTATTCCATGGCGGTGATGTAGCGCCATATAGAGCATGATAAACGCCAGCCGCTACCGTTGGTCATCCCGATGCTATTTTATCACGGTAGCCGTAGTCCTTACCCCTGGTCCCTGTGCTGGCTGGACGAATTTGCCGACCCGACTACCGCACGG  >  NC_000913/4569173‑4569441                                                                                                                                         |                                                                                                                                     cgcTACACTCCGATATTTTATGGTCGGTAAAGACCCGCGAAGGCGATGGCTATATCTATGTGGTGATTGAACATCAGAGCCGCGAGGACATTCATATGGCCTTTCGCCTGATGCGCTATTCCATGGCGGTGATGTAacg                                                                                                                                    <  1:548243/139‑1 (MQ=255)             atatTTTATGGTCGGTAAAGACCCGCGAAGGCGATGGCTATATCTATGTGGTGATTGAACATCAGAGCCGCGAGGACATTCATATGGCCTTTCGCCTGATGCGCTATTCCATGGCGGTGATGTAACGCCATATAGAGCa                                                                                                                        >  1:440624/1‑139 (MQ=255)                     tGGTCGGTAAAGACCCGCGAAGGCGATGGCTATATCTATGTGGTGATTGAACATCAGAGCCGCGAGGACATTCATATGGCCTTTCGCCTGATGCGCTATTCCATGGCGGTGATGTAACGCCATATAGAGCa                                                                                                                        <  2:827330/131‑1 (MQ=255)                     tGGTCGGTAAAGACCCGCGAAGGCGATGGCTATATCTATGTGGTGATTGAACATCAGAGCCGCGAGGACATTCATATGGCCTTTCGCCTGATGCGCTATTCCATGGCGGTGATGTAACGCCATATAGAGCa                                                                                                                        >  1:827330/1‑131 (MQ=255)                        tCGGTAAAGACCCGCGAAGGCGATGGCTATATCTATGTGGTGATTGAACATCAGAGCCGCGAGGACATTCATATGGCCTTTCGCCTGATGCGCTATTCCATGGCGGTGATGTAACGCCATATAGAGCATGATAAACGcc                                                                                                             <  2:349668/139‑1 (MQ=255)                          ggTAAAGACCCGCGAAGGCGATGGCTATATCTATGTGGTGATTGAACATCAGAGCCGCGAGGACATTCATATGGCCTTTCGCCTGATGCGCTATTCCATGGCGGTGATGTAACGCCATATAGAGCATGATAAACGCCAg                                                                                                           >  1:255733/1‑139 (MQ=255)                                        aaGGCGATGGCTATATCTATGTGGTGATTGAACATCAGAGCCGCGAGGACATTCATATGGCCTTTCGCCTGATGCGCTATTCCATGGCGGTGATGTAACGCCATATAGAGCATGATAAACGCCAGCCGCTACCGTTGGt                                                                                             <  2:255733/139‑1 (MQ=255)                                                           tgtgGTGATTGAACATCAGAGCCGCGAGGACATTCATATGGCCTTTCGCCTGATGCGCTATTCCATGGCGGTGATGTAACGCCATATAGAGCATGATAAACGCCAGCCGCTACCGTTGGTCATCCCGATGCTATTTTAt                                                                          >  1:95574/1‑139 (MQ=255)                                                           tgtgGTGATTGAACATCAGAGCCGCGAGGACATTCATATGGCCTTTCGCCTGATGCGCTATTCCATGGCGGTGATGTAACGCCATATAGAGCATGATAAACACCAGCCGCTACCGTTGGTCATCCCGATGCTATTTTAt                                                                          >  2:516322/1‑139 (MQ=255)                                                            gtggtgATTAAACATCAGAGCCGCGAGGACATTCATATGGCCTTTCGCCTGATGCGCTATTCCATGGCGGTGATGTAACGCCATATAGAGCATGATAAACGCCAGCCGCTACCGTTGGTCATCCCGATGCTATTTTATc                                                                         >  2:677453/1‑139 (MQ=255)                                                               gtgATTGAACATCAGAGCCGCGAGGACATTCATATGGCCTTTCGCCTGATGCGCTATTCCATGGCGGTGATGTAACGCCATATAGAGCATGATAAACGCCAGCCGCTACCGTTGGTCATCCCGATGCTATTTTATCACg                                                                      >  2:162993/1‑139 (MQ=255)                                                               gtgATTGAACATCAGAGCCGCGAGGACATTCATATGGCCTTTCGCCTGATGCGCTATTCCATGGCGGTGATGTAACGCCATATAGAGCATGATAAACGCCAGCCGCTACCGTTGGTCATCCCGATGCTATTTTATCACg                                                                      >  2:819425/1‑139 (MQ=255)                                                                       aCATCAGAGCCGCGAGGACATTCATATGGCCTTTCGCCTGATGCGCTATTCCATGGCGGTGATGTAACGCCATATAGAGCATGATAAACGCCAGCCGCTACCGTTGGTCATCCCGATGCTATTTTGTCACGGTAGCCGt                                                              <  1:677453/139‑1 (MQ=255)                                                                       aCATCAGAGCCGCGAGGACATTCATATGGCCTTTCGCCTGATGCGCTATTCCATGGCGGTGATGTAACGCCATATAGAGCATGATAAACGCCAGCCGCTACCGTTGGTCATCCCGATGCTATTTTATCACGGTAGCCGt                                                              <  1:162993/139‑1 (MQ=255)                                                                            agagCCGCGAGGACATTCATATGGCCTTTCGCCTGATGCGCTATTCCATGGCGGTGATGTAacg                                                                                                                                    >  1:16135/1‑64 (MQ=255)                                                                            agagCCGCGAGGACATTCATATGGCCTTTCGCCTGATGCGCTATTCCATGGCGGTGATGTAacg                                                                                                                                    <  2:16135/64‑1 (MQ=255)                                                                             gagCCGCGAGGACATTCATATGGCCTTTCGCCTGATGCGCTATTCCATGGCGGTGATGTAACGCCATATAGAGCATGATAAACGCCAGCCGCTACCGTTGGTCATCCCGATGCTATTTTATCACGGTAGCCGTAGTCCt                                                        <  2:95574/139‑1 (MQ=255)                                                                                   cgAGGACATTCATATGGCCTTTCGCCTGATGCGCTATTCCATGGCGGTGATGTAACGCCATATAGAGCATGATAAACGCCAGCCGCTACCGTTGGTCATCCCGATGCTATTTTATCACGGTAGCCGTAGTCCTTAcccc                                                  >  2:363591/1‑139 (MQ=255)                                                                                     aGGACATTCATATGGCCTTTCGCCTGATGCGCTATTCCATGGCGGTGATGTAACGCCATATAGAGCATGATAAACGCCAGCCGCTACCGTTGGTCATCCCGATGCTATTTTATCACGTTAGCCGTAGTCCt                                                        >  2:594521/1‑131 (MQ=255)                                                                                     aGGACATTCATATGGCCTTTCGCCTGATGCGCTATTCCATGGCGGTGATGTAACGCCATATAGAGCATGATAAACGCCAGCCGCTACCGTTGGTCATCCCGATGCTATTTGATCACGGTAGCCGTAGTCCt                                                        <  1:594521/131‑1 (MQ=255)                                                                                         cATTCATATGGCCTTTCGCCTGATGCGCTATTCCATGGCGGTGATGTAACGCCATATAGAGCATGATAAACGCCAGCCGCTACCGTTGGTCATCCCGATGCTATTTTATCACGGTAGCCGTAGTCCTTACCCCTGGTcc                                            <  1:217752/139‑1 (MQ=255)                                                                                                  ggCCTTTCGCCTGATGCGCTATTCCATGGCGGTGATGTAACGCCATATAGAGCATGATAAACGCCAGCCGCTACCGTTGGTCATCCCGATGCTATTTTATCACGGTAGCCGTAGTCCTTACCCCTGGTCCCTGTgctgg                                   <  1:363591/139‑1 (MQ=255)                                                                                                   gCCTTTCGCCTGATGCGCTATTCCATGGCGGTGATGTAACGCCATATAGAGCATGATAAACGCCAGCCGCTACCGTTGGTCATCCCGATGCTATTTTATCACGGTAGCCGTAGTCCt                                                        <  1:938812/117‑1 (MQ=255)                                                                                                   gCCTTTCGCCTGATGCGCTATTCCATGGCGGTGATGTAACGCCATATAGAGCATGATAAACGCCAGCCGCTACCGTTGGTCATCCCGATGCTATTTTATCACGGTAGCCGTAGTCCt                                                        >  2:938812/1‑117 (MQ=255)                                                                                                    ccTTTCGCCTGATGCGCTATTCCATGGCGGTGATGTAACGCCAtata                                                                                                                             <  1:810864/47‑1 (MQ=255)                                                                                                    ccTTTCGCCTGATGCGCTATTCCATGGCGGTGATGTAACGCCAtata                                                                                                                             >  2:810864/1‑47 (MQ=255)                                                                                                    ccTTTCGCCTGATGCGCTATTCCATGGCGGTGATGTAACGCCATATAGAGCa                                                                                                                        >  1:437042/1‑52 (MQ=255)                                                                                                    ccTTTCGCCTGATGCGCTATTCCATGGCGGTGATGTAACGCCATATAGAGCa                                                                                                                        <  2:437042/52‑1 (MQ=255)                                                                                                    ccTTTCGCCTGATGCGCTATTCCATGGCGGTGATGTAACGCCATATAGAGCATGATAAACGCCAGCCGCTACCGTTGGTCATCCCGATGCTATTTTATCACGGt                                                                    >  2:980279/1‑104 (MQ=255)                                                                                                    ccTTTCGCCTGATGCGCTATTCCATGGCGGTGATGTAACGCCATATAGAGCATGATAAACGCCAGCCGCTACCGTTGGTCATCCCGATGCTATTTTATCACGGt                                                                    <  1:980279/104‑1 (MQ=255)                                                                                                    ccTTTCGCCTGATGCGCTATTCCATGGCGGTGATGTAACGCCATATAGAGCATGATAAACGCCAGCCGCTACCGTTGGTCATCCCGATGCTATTTTATCACGGTAGCCGTAGTCCTTACCCCTGGTCCCTGTgctggct                                 >  1:92029/1‑139 (MQ=255)                                                                                                    ccTTTCGCCTGATGCGCTATTCCATGGCGGTGATGTAACGCCATATAGAGCATGATAAACGCCAGCCGCTACCGTTGGTCATCCCGATGCTATTTTATCACGGTAGCCGTAGTCCTTACCCCTGGTCCCTGTgctggct                                 >  1:337853/1‑139 (MQ=255)                                                                                                      tttCGCCTGATGCGCTATTCCATGGCGGTGATGTAACGCCATATAGAGCATGATAAACGCCAGCCGCTACCGTTGGTCATCCCGATGCTATTTTATCACGGt                                                                    <  2:487703/102‑1 (MQ=255)                                                                                                      tttCGCCTGATGCGCTATTCCATGGCGGTGATGTAACGCCATATAGAGCATGATAAACGCCAGCCGCTACCGTTGGTCATCCCGATGCTATTTTATCACGGt                                                                    >  1:487703/1‑102 (MQ=255)                                                                                                        tCGCCTGATGCGCTATTCCATGGCGGTGATGTAACGCCATATAGAGCATGATAAACGCCAGCCGCTACCGTTGGTCATCCCGATGCTATTTTATCACGGTAGCCGTAGTCCTTACCCCTGGTCCCTGTGCTGGCTGGAc                             >  2:551017/1‑139 (MQ=255)                                                                                                                        tCCATGGCGGTGATGTAACGCCATATAGAGCATGATAAACGCCAGCCGCTACCGTTGGTCATCCCGATGCTATTTTATCACGGt                                                                    >  2:745536/1‑84 (MQ=255)                                                                                                                        tCCATGGCGGTGATGTAACGCCATATAGAGCATGATAAACGCCAGCCGCTACCGTTGGTCATCCCGATGCTATTTTATCACGGt                                                                    <  1:745536/84‑1 (MQ=255)                                                                                                                               cGGTGATGTAACGCCATATAGAGCATGATAAACGCCAGCCGCTACCGTTGGTCATCCCGATGCTATTTTATCACGGTAGCCGTAGTCCTTACCCCTGGTCCCTGTGCTGGCTGGACGAATTTGCCGACCCGACTACCGc      >  2:48592/1‑139 (MQ=255)                                                                                                                                 gTGATGTAACGCCATATAGAGCATGATAAACGCCAGCCGCTACCGTTGGTCATCCCGATGCTATTTTATCACGGTAGCCGTAGt                                                           >  2:380014/1‑84 (MQ=255)                                                                                                                                 gTGATGTAACGCCATATAGAGCATGATAAACGCCAGCCGCTACCGTTGGTCATCCCGATGCTATTTTATCACGGTAGCCGTAGt                                                           <  1:380014/84‑1 (MQ=255)                                                                                                                                 gTGATGTAACGCCATATAGAGCATGATAAACGCCAGCCGCTACCGTTGGTCATCCCGATGCTATTTTATCACGGTAGCCGTAGTCCTTACCCCTGGTCCCTGTGCTGGCTGGACGAATTTGCCGACCCGACTACCGCAc    >  1:984003/1‑139 (MQ=255)                                                                                                                                  tGATGTAACGCCATATAGAGCATGATAAACGCCAGCCGCTACCGTTGGTCATCCCGATGCTATTTTATCACGGTAGCCGTAGTCCTTACCCCTGGTCCCTGTGCTGGCTGGACGAATTTGCCGACCCGACTACCGCACg   >  1:127597/1‑139 (MQ=255)                                                                                                                                   gATGTAACGCCATATAGAGCATGATAAACGCCAGCCGCTACCGTTGGTCATCCCGATGCTATTTTATCACGGTAGCCGTAGTCCTTACCCCTGGTCCCTGTGCTGGCTGGACGAATTTGCCGACCCGACTACCGCACgg  <  1:551017/139‑1 (MQ=255)                                                                                                                                         |                                                                                                                                     CGCTACACTCCGATATTTTATGGTCGGTAAAGACCCGCGAAGGCGATGGCTATATCTATGTGGTGATTGAACATCAGAGCCGCGAGGACATTCATATGGCCTTTCGCCTGATGCGCTATTCCATGGCGGTGATGTAGCGCCATATAGAGCATGATAAACGCCAGCCGCTACCGTTGGTCATCCCGATGCTATTTTATCACGGTAGCCGTAGTCCTTACCCCTGGTCCCTGTGCTGGCTGGACGAATTTGCCGACCCGACTACCGCACGG  >  NC_000913/4569173‑4569441

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑