Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,347,069	G→A	*164* (TAG→TAA)	ptsN →	sugar‑specific enzyme IIA component of PTS

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,347,069	0	G	A	100.0%	177.0 / NA	55	*164* (TAG→TAA)	ptsN	sugar‑specific enzyme IIA component of PTS
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (27/28);  total (27/28)

ACCTGCATACTCTGTCGCTGGTGGCGAAACGTCTGGCGGACAAAACCATCTGCCGCCGTTTACGCGCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAGTTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCGGACGTTCAGGTTCAGGTAAATCTGTCGCCCTGCGTGCGCTGGAAGATATGGGTTTTTACTGCGTG  >  NC_000913/3346936‑3347201                                                                                                                                      |                                                                                                                                     aCCTGCATACTCTGTCGCTGGTGGCGAAACGTCTGGCGGACAAAACCATCTGCCGCCGTTTACGCGCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAattatt                                                                                                                                 >  1:926242/1‑139 (MQ=255) aCCTGCATACTCTGTCGCTGGTGGCGAAACGTCTGGCGGACAAAACCATCTGCCGCCGTTTACGCGCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAattatt                                                                                                                                 <  2:193845/139‑1 (MQ=255)          ctctGTCGCTGGTGGCGAAACGTCTGGCGGACAAAACCATCTGCCGCCGTTTACGCGCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGt                                                                                                                        <  2:926242/139‑1 (MQ=255)               tCGCTGGTGGCGAAACGTCTGGCGGACAAAACCATCTGCCGCCGTTTACGCGCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGt                                                                                                                             >  2:381787/1‑129 (MQ=255)               tCGCTGGTGGCGAAACGTCTGGCGGACAAAACCATCTGCCGCCGTTTACGCGCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGt                                                                                                                             <  1:381787/129‑1 (MQ=255)                 gCTGGTGGCGAAACGTCTGGCGGACAAAACCATCTGCCGCCGTTTACGCGCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCtttt                                                                                                                 >  2:286646/1‑139 (MQ=255)                         cGAAACGTCTGGCGGACAAAACCATCTGCCGCCGTTTACGCGCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTtg                                                                                                         >  2:1345047/1‑139 (MQ=255)                                tCTGGCGGACAAAACCATCTGCCGCCGTTTACGCGCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTgaggag                                                                                                  <  1:286646/139‑1 (MQ=255)                                     cGGACAAAACCATCTGCCGCCGTTTACGCGCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACa                                                                                             <  1:183969/139‑1 (MQ=255)                                        aCAAAACCATCTGCCGCCGTTTACGCGCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAAt                                                                                                                          >  2:601386/1‑107 (MQ=255)                                        aCAAAACCATCTGCCGCCGTTTACGCGCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAAt                                                                                                                          <  1:601386/107‑1 (MQ=255)                                             aCCATCTGCCGCCGTTTACGCGCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATgg                                                                                     <  2:216610/139‑1 (MQ=255)                                                aTCTGCCGCCGTTTACGCGCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTAc                                                                                  <  2:135924/139‑1 (MQ=255)                                                      cgccgTTTACGCGCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCtttt                                                                                                                 >  1:649617/1‑102 (MQ=255)                                                      cgccgTTTACGCGCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCtttt                                                                                                                 <  2:649617/102‑1 (MQ=255)                                                                     gCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCGGACgtt                                                             <  1:1345047/139‑1 (MQ=255)                                                                      cccAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTAc                                                                                  <  1:314147/117‑1 (MQ=255)                                                                      cccAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTAc                                                                                  >  2:314147/1‑117 (MQ=255)                                                                                       cTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGt                                                                                                                        >  2:813478/1‑62 (MQ=255)                                                                                       cTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGt                                                                                                                        <  1:813478/62‑1 (MQ=255)                                                                                          tATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCGGACGTTCAGGTTCAGGTAAATCTGTCg                                        >  2:1118455/1‑139 (MQ=255)                                                                                                    ttACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGt                                                                                                                        <  2:1186301/49‑1 (MQ=255)                                                                                                    ttACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGt                                                                                                                        >  1:1186301/1‑49 (MQ=255)                                                                                                    ttACGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCGGACGTTCAGGTTCAGGTAAATCTGTCGCCCtgcgtgc                              >  2:207350/1‑139 (MQ=255)                                                                                                      aCGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACg                                                                                                            >  1:1244942/1‑59 (MQ=255)                                                                                                      aCGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACg                                                                                                            <  2:1244942/59‑1 (MQ=255)                                                                                                      aCGGATACCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCGGACGTTCAGGTTCAGGTAAATCTGTCGCCCTGCGTgcgc                            >  2:583506/1‑139 (MQ=255)                                                                                                          aTACCGAAGGTACTCCAGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTAc                                                                                  <  2:1265374/81‑1 (MQ=255)                                                                                                          aTACCGAAGGTACTCCAGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTAc                                                                                  >  1:1265374/1‑81 (MQ=255)                                                                                                            aCCGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCGGACGTTCAGGTTCAGGTAAATCTGTCGCCCTGCGTGCGCTGGAAg                      >  2:707/1‑139 (MQ=255)                                                                                                              cGAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCGGACGTTCAGGTTCAGGTAAATCTGTCGCCCTGCGTGCGCTGGAAGat                    >  2:183341/1‑139 (MQ=255)                                                                                                               gAAGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCGGACGTTCAGGTTCAGGTAAATCTGTCGCCCTGCGTGCGCTGGAAGata                   <  1:707/139‑1 (MQ=255)                                                                                                                aaGGTACTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCGGACGTTCAGGTTCAGGTAAATCTGTCGCCCTGCGTGCGCTGGAAGatat                  >  2:761835/1‑139 (MQ=255)                                                                                                                      cTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCGGACGTTCAGGTTCAGGTAAATCTGTCGCCCTGCGTGCGCTgg                         >  1:109440/1‑126 (MQ=255)                                                                                                                      cTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCGGACGTTCAGGTTCAGGTAAATCTGTCGCCCTGCGTGCGCTgg                         <  2:109440/126‑1 (MQ=255)                                                                                                                      cTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCGGACGTTCAGGTTCAGGTAAATCTGTCGCCCTGCGTGCGCTGGAAGata                   <  1:327650/132‑1 (MQ=255)                                                                                                                      cTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCGGACGTTCAGGTTCAGGTAAATCTGTCGCCCTGCGTGCGCTGGAAGata                   >  2:327650/1‑132 (MQ=255)                                                                                                                      cTCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCGGACGTTCAGGTTCAGGTAAATCTGTCGCCCTGCGTGCGCTGGAAGATATGGGttt            >  2:973005/1‑139 (MQ=255)                                                                                                                      cTCCGGATGAAGCATAATTATTCGGTAATGTCT‑TTTTAGACGTTGTgagg                                                                                                    >  2:25062/1‑50 (MQ=255)                                                                                                                      cTCCGGATGAAGCATAATTATTCGGTAATGTCT‑TTTTAGACGTTGTgagg                                                                                                    <  1:25062/50‑1 (MQ=255)                                                                                                                       tCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGgaga                                                                                                 <  2:983897/53‑1 (MQ=255)                                                                                                                       tCCGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGgaga                                                                                                 >  1:983897/1‑53 (MQ=255)                                                                                                                        ccGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATg                                                                                      >  1:343953/1‑63 (MQ=255)                                                                                                                        ccGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATg                                                                                      <  2:343953/63‑1 (MQ=255)                                                                                                                        ccGGATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCGGACGTTCAGGTTCAGGTAAATCTGTCGCCCTGCGTGCGCTGGAAGATATGGGttttt          >  1:871893/1‑139 (MQ=255)                                                                                                                           gATGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCGGACGTTCAGGTTCAGGTAAATCTGTCGCCCTGCGTGCGCTGGAAGATATGGGTTTTTACt       <  1:761835/139‑1 (MQ=255)                                                                                                                            aTGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGaaa                                                                                               >  2:926565/1‑50 (MQ=255)                                                                                                                            aTGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGaaa                                                                                               <  1:926565/50‑1 (MQ=255)                                                                                                                            aTGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCGGACGTTCAGGTTCAGGTAAATCTGTCGCCCTGCGTGCGCTGGAAGATATGGGTTTTTACTg      <  1:207350/139‑1 (MQ=255)                                                                                                                            aTGAAGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCGGACGTTCAGGTTCAGGTAAATCTGTCGCCCTGCGTGCGCTGGAAGATATGGGTTTTTACTg      <  1:973005/139‑1 (MQ=255)                                                                                                                               aaGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCGGACgt                                                              <  1:781405/80‑1 (MQ=255)                                                                                                                               aaGCGTAATTACTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCGGACgt                                                              >  2:781405/1‑80 (MQ=255)                                                                                                                                aGCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCGGACGTTCAGGTTCAGGTAAATCTGTCGCCCTGCGTGCGCTGGAAGATATGGGTTTTTACTGCGTg  <  1:183341/139‑1 (MQ=255)                                                                                                                                 gCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTgaggag                                                                                                  <  2:435776/42‑1 (MQ=255)                                                                                                                                 gCGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTgaggag                                                                                                  >  1:435776/1‑42 (MQ=255)                                                                                                                                  cGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCGGACGTTCAGGTTCAGGTAAATCTGTCGCCCtgcgtgcg                             <  2:354039/110‑1 (MQ=255)                                                                                                                                  cGTAATTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCGGACGTTCAGGTTCAGGTAAATCTGTCGCCCtgcgtgcg                             >  1:354039/1‑110 (MQ=255)                                                                                                                                      |                                                                                                                                     ACCTGCATACTCTGTCGCTGGTGGCGAAACGTCTGGCGGACAAAACCATCTGCCGCCGTTTACGCGCAGCCCAGAGCGATGAAGAGCTGTATCAAATCATTACGGATACCGAAGGTACTCCGGATGAAGCGTAGTTATTCGGTAATGTCTCTTTTAGACGTTGTGAGGAGAAACAGTACATGGTACTGATGATCGTCAGCGGACGTTCAGGTTCAGGTAAATCTGTCGCCCTGCGTGCGCTGGAAGATATGGGTTTTTACTGCGTG  >  NC_000913/3346936‑3347201

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑