Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A9 F1 I1 R1 759 71.0 3673240 91.5% 3361014 104.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,685,561 T→C intergenic (‑54/‑274) glyA ← / → hmp serine hydroxymethyltransferase/fused nitric oxide dioxygenase/dihydropteridine reductase 2

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,685,5610TC100.0% 210.5 / NA 58intergenic (‑54/‑274)glyA/hmpserine hydroxymethyltransferase/fused nitric oxide dioxygenase/dihydropteridine reductase 2
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (29/29);  total (29/29)

TGACGTACTTTTTCCTGCTCCATAGCCTGCCACAGTTCGGCATCATAATCGGCAATGTTCATTTCACGCTTTAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCTGTTGGACAACGGCGAACAGTATAACCGAATCATTGTGCGATAACAGGTCTTGACAAAGGAATTTACGCAAACGATTACCTTCAGGCTACGCAAGGCTTTGGAGAATAAAGAGCTTGCAACCGGAAACGGATTTC  >  NC_000913/2685431‑2685695
                                                                                                                                  |                                                                                                                                      
tGACGTACTTTTTCCTGCTCCATAGCCTGCCACAGTTCGGCATCATAATCGGCAATGTTCATTTCACGCTTTAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACa                                                                                                                                <  1:944426/139‑1 (MQ=255)
   cGTACTTTTTCCTGCTCCATAGCCTGCCACAGTTCGGCATCATAATCGGCAATGTTCATTTCACGCTTTAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACg                                                                                                                             <  1:1480209/139‑1 (MQ=255)
    gTACTTTTTCCTGCTCCATAGCCTGCCACAGTTCGGCATCATAAACGGCAATGTTCATTTCACGCTTTAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACgg                                                                                                                            >  2:733074/1‑139 (MQ=255)
              cTGCTCCATAGCCTGCCACAGTTCGGCATCATAATCGGCAATGTTCATTTCACGCTTTAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGAACAGtat                                                                                                                  <  1:708207/139‑1 (MQ=255)
                 cTCCATAGCCTGCCACAGTTCGGCATCATAATCGGCAATGTTCATTTCACGCTTTAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCg                                                                                                                          <  1:1293534/128‑1 (MQ=255)
                 cTCCATAGCCTGCCACAGTTCGGCATCATAATCGGCAATGTTCATTTCACGCTTTAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCg                                                                                                                          >  2:1293534/1‑128 (MQ=255)
                     aTAGCCTGCCACAGTTCGGCATCATAAACGGCAATGTTCATTTCACGCTTTAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGAACAGTATAACCGaa                                                                                                           <  1:733074/139‑1 (MQ=255)
                      tAGCCTGCCACAGTTCGGCATCATAATCGGCAATGTTCATTTCACGCTTTAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGa                                                                                                                         >  2:662991/1‑124 (MQ=255)
                      tAGCCTGCCACAGTTCGGCATCATAATCGGCAATGTTCATTTCACGCTTTAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGa                                                                                                                         <  1:662991/124‑1 (MQ=255)
                      tAGCCTGCCACAGTTCGGCATCATAATCGGCAATGTTCATTTCACGCTTTAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGAACAGTATAACCGAAt                                                                                                          >  2:1662913/1‑139 (MQ=255)
                           tGCCACAGTTCGGCATCATAATCGGCAATGTTCATTTCACGCTTTAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGAACAGtat                                                                                                                  <  2:309563/126‑1 (MQ=255)
                           tGCCACAGTTCGGCATCATAATCGGCAATGTTCATTTCACGCTTTAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGAACAGtat                                                                                                                  >  1:309563/1‑126 (MQ=255)
                             ccACAGTTCGGCATCATAATCGGCAATGTTCATTTCACGCTTTAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGAACAGTATAACCGAATCATtgtg                                                                                                   >  2:1388285/1‑139 (MQ=255)
                              cacaGTTCGGCATCATAATCGGCAATGTTCATTTCACGCTTTAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACa                                                                                                                                <  2:1258144/109‑1 (MQ=255)
                              cacaGTTCGGCATCATAATCGGCAATGTTCATTTCACGCTTTAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACa                                                                                                                                >  1:1258144/1‑109 (MQ=255)
                              cacaGTTCGGCATCATAATCGGCAATGTTCATTTCACGCTTTAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCg                                                                                                                          <  1:1031694/115‑1 (MQ=255)
                              cacaGTTCGGCATCATAATCGGCAATGTTCATTTCACGCTTTAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCg                                                                                                                          >  2:1031694/1‑115 (MQ=255)
                                   ttCGGCATCATAATCGGCAATGTTCATTTCACGCTTTAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGAACAGTATAACCGAATCATTGTGCGATaa                                                                                             <  1:1388285/139‑1 (MQ=255)
                                        catcatAATCGGCAATGTTCATTTCACGCTTTAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGAACAGTATAACCGAATCATTGTGCGATAACAGGt                                                                                        >  2:789657/1‑139 (MQ=255)
                                                  ggCAATGTTCATTTCACGCTTTAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGAACAGTATAACCGAATCAt                                                                                                       <  2:1596298/114‑1 (MQ=255)
                                                  ggCAATGTTCATTTCACGCTTTAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGAACAGTATAACCGAATCAt                                                                                                       >  1:1596298/1‑114 (MQ=255)
                                                      aTGTTCATTTCACGCTTTAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGAACAGTATAACCGAATCATTGTGCGATAACAGGTCTTGACAAAGGAAt                                                                          >  2:1469201/1‑139 (MQ=255)
                                                      aTGTTCATTTCACGCTTTAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGAACAGTATAACCGAATCATTGTGCGATAACAGGTCTTGACAAAGGAAt                                                                          >  2:1556485/1‑139 (MQ=255)
                                                         ttCATTTCACGCTTTAACATCCGCATCTCCTGACTCACCTTACCATAAAACTTCTGGCATTTATAGGCGGTACCATTGGTCAAAGGAGAACCATATAACCGAATAATTGTGCCATAACAATCCCTGAAAAAGGaagtaa                                                                       >  1:146772/1‑135 (MQ=255)
                                                            aTTTCACGCTTTAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGAACAGTATAACCGAATCATtgtg                                                                                                   >  2:1432570/1‑108 (MQ=255)
                                                            aTTTCACGCTTTAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGAACAGTATAACCGAATCATtgtg                                                                                                   <  1:1432570/108‑1 (MQ=255)
                                                               tCACGCTTTAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGAACAGTATAACCGAATCATTGTGCGATAACAGGTCTTGACAAAGGAATTTACGCaaa                                                                 <  1:789657/139‑1 (MQ=255)
                                                                 aCGCTTTAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGAACAGTATAACCGAATCATTGTGc                                                                                                  <  2:929784/104‑1 (MQ=255)
                                                                 aCGCTTTAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGAACAGTATAACCGAATCATTGTGc                                                                                                  >  1:929784/1‑104 (MQ=255)
                                                                             ccGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGAACAGTATAACCGAATCATTGTGCGATAACAGGTCTTGACAAAGGAATTTACGCAAACGAt                                                             >  2:1713065/1‑129 (MQ=255)
                                                                             ccGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGAACAGTATAACCGAATCATTGTGCGATAACAGGTCTTGACAAAGGAATTTACGCAAACGAt                                                             <  1:1713065/129‑1 (MQ=255)
                                                                               gCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGAACAGTATAACCGAATCATTGTGCGATAACAGGTCTTGACAAAGGAATTTACGCAAACGATTACCt                                                        >  1:889294/1‑132 (MQ=255)
                                                                               gCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGAACAGTATAACCGAATCATTGTGCGATAACAGGTCTTGACAAAGGAATTTACGCAAACGATTACCt                                                        <  2:889294/132‑1 (MQ=255)
                                                                               gCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGAACAGTATAACCGAATCATTGTGCGATAACAGGTCTTGACAAAGGAATTTACGCAAACGATTACCTTCAGGCt                                                 >  1:668441/1‑139 (MQ=255)
                                                                                 aTCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGAACAGTATAACCAAATCATTGTGCGATAACAGGTCTTGACAAAGGAAtt                                                                         >  2:1102549/1‑113 (MQ=255)
                                                                                 aTCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGAACAGTATAACCAAATCATTGTGCGATAACAGGTCTTGACAAAGGAAtt                                                                         <  1:1102549/113‑1 (MQ=255)
                                                                                    tcCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGAACAGTATAACCGAATCATTGTGCGATAACAGGTCTTGACAAAGGAATTTACGCAAACGATTACCTTCAGGCTACGCa                                            <  2:668441/139‑1 (MQ=255)
                                                                                    tcCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGAACAGTATAACCGAATCATTGTGCGATAACAGGTCTTGACAAAGGAATTTACGCAAACGATTACCTTCAGGCTACGCa                                            <  1:1469201/139‑1 (MQ=255)
                                                                                    tcCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGAACAGTATAACCGAATCATTGTGCGATAACAGGTCTTGACAAAGGAATTTACGCAAACGATTACCTTCAGGCTACGCa                                            <  1:1662913/139‑1 (MQ=255)
                                                                                     ccTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGAACAGTATAACCGAATCATTGTGCGATAACAGGTCTTGACAAAGGAATTTACGCAAACGATTACCTTCAGGCTACGCaa                                           >  1:1827672/1‑139 (MQ=255)
                                                                                      cTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGAACAGTATAACCGAATCATTGTGCGATAACAGGt                                                                                        >  1:895220/1‑93 (MQ=255)
                                                                                      cTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGAACAGTATAACCGAATCATTGTGCGATAACAGGt                                                                                        <  2:895220/93‑1 (MQ=255)
                                                                                         aCTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGAACAGTATAACCGAATCATTGTGCGATAACAGGTCTTGACAAAGGAATTTACGCAAACGATTACCTTCAGGCTACGCAAGGCt                                       <  2:1827672/139‑1 (MQ=255)
                                                                                             aGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCg                                                                                                                          <  2:858218/52‑1 (MQ=255)
                                                                                             aGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCg                                                                                                                          >  1:858218/1‑52 (MQ=255)
                                                                                             aGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGAACAGTATAACCGAATCATTGTGCGATAACAGGTCTTGACAAAGGAATTTACGCAAACGAt                                                             >  2:542100/1‑113 (MQ=255)
                                                                                             aGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGAACAGTATAACCGAATCATTGTGCGATAACAGGTCTTGACAAAGGAATTTACGCAAACGAt                                                             <  1:542100/113‑1 (MQ=255)
                                                                                             aGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCCGTTGGACAACGGCGAACAGTATAACCGAATCATTGTGCGATAACAGGTCTTGACAAAGGAATTTACGCAAACGATTACCTTCAGGCTACGCAAGGCTTTgg                                   >  2:745910/1‑139 (MQ=255)
                                                                                                              ttGGCCTTTATAGGCGGTCCCGTTGGACAACGGCg                                                                                                                          >  2:1458634/1‑35 (MQ=255)
                                                                                                              ttGGCCTTTATAGGCGGTCCCGTTGGACAACGGCg                                                                                                                          <  1:1458634/35‑1 (MQ=255)
                                                                                                                             ggTCCCGTTGGACAACGGCGAACAGTATAACCGAATCATTGTGCGATAACAGGTCTTGACAAAGGAATTTACGCAAACGATTACCTTCAGGCTACGCAAGGCTTTGGAGAATAAAGAGCTTGCAACCGGAAACGGAttt   >  2:1409787/1‑139 (MQ=255)
                                                                                                                              gTCCCGTTGGACAACGGCGAACAGTATAACCGAATCATTGTGCGATAACAGGTCTTGACAAAGGAATTTACGCAAACGATTACCTTCAGGCTACGCAAGGCttt                                     >  1:1246585/1‑104 (MQ=255)
                                                                                                                              gTCCCGTTGGACAACGGCGAACAGTATAACCGAATCATTGTGCGATAACAGGTCTTGACAAAGGAATTTACGCAAACGATTACCTTCAGGCTACGCAAGGCTTTGGAGAATAAAGAGCTTGCAACCGGAAACGGATTTc  >  1:1529513/1‑139 (MQ=255)
                                                                                                                              gTCCCGTTGGACAACGGCGAACAGTATAACCGAATCATTGTGCGATAACAGGTCTTGACAAAGGAATTTACGCAAACGATTACATTCAGGCTACGCAAGGtttt                                     <  2:1246585/104‑1 (MQ=255)
                                                                                                                               tCCCGTTGGACAACGGCGAACAGTATAACCGAATCATTGTGCGATAACAGGTCTTGACaaa                                                                               >  1:190316/1‑61 (MQ=255)
                                                                                                                               tCCCGTTGGACAACGGCGAACAGTATAACCGAATCATTGTGCGATAACAGGTCTTGACaaa                                                                               <  2:190316/61‑1 (MQ=255)
                                                                                                                               tCCCGTTGGACAACGGCGAACAGTATAACCGAATCATTGTGCGATAACAGGTCTTGACAAAGGAATTTACGCAAACGAt                                                             <  2:577764/79‑1 (MQ=255)
                                                                                                                               tCCCGTTGGACAACGGCGAACAGTATAACCGAATCATTGTGCGATAACAGGTCTTGACAAAGGAATTTACGCAAACGAt                                                             <  2:787553/79‑1 (MQ=255)
                                                                                                                                  |                                                                                                                                      
TGACGTACTTTTTCCTGCTCCATAGCCTGCCACAGTTCGGCATCATAATCGGCAATGTTCATTTCACGCTTTAACATCCGCATCTCCTGACTCAGCTAACAATAAAATTTTTGGCCTTTATAGGCGGTCCTGTTGGACAACGGCGAACAGTATAACCGAATCATTGTGCGATAACAGGTCTTGACAAAGGAATTTACGCAAACGATTACCTTCAGGCTACGCAAGGCTTTGGAGAATAAAGAGCTTGCAACCGGAAACGGATTTC  >  NC_000913/2685431‑2685695

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A