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
A12 F1 I2 R1 766 55.6 2631458 94.7% 2491990 109.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,271,455 G→A T132I (ACC→ATC)  chaA ← calcium/sodium:proton antiporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,271,4550GA100.0% 180.9 / NA 56T132I (ACC→ATC) chaAcalcium/sodium:proton antiporter
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (28/28);  total (28/28)

TTAATGCTACCAGTAACGCCTGACCGGTTGAAAAATTCGCCGCAGGCAGAGCCATTGGAAATACCAGTACGATTATCGCCAGGGGGAACAGCGCAATTAAATACTGCTTGATACCAAACAGATTCATATATTGGGTGGCAAACTTACGACCGCCCAACAATAATGAAAAGCCAACCAGCCCACCGGTAACAATCATAATGATTGAATAGAGCGTATCACGCATTAGCGTTGGCGCGGCGTCGCCGGTTGCCATTAAAGCTGAAATCAAAC  >  NC_000913/1271321‑1271590
                                                                                                                                      |                                                                                                                                       
ttAATGCTACCAGTAACGCCTGACCGGTTGAAAAATTCGCCGCAGGCAGAGCCATTGGAAATACCAGTACGATTATCGCCAGGGGGAACAGCGCAATTAAATACTGCTTGATACCAAACAGATTCATATATTGGATGGc                                                                                                                                     <  1:956873/139‑1 (MQ=255)
        aCCAGTAACGCCTGACCGGTTGAAAAATTCGCCGCAGGCAGAGCCATTGGAAATACCAGTACGATTATCGCCAGGGGGAACAGCGCAATTAAATACTGCTTGATACCAAACAGATTCATATATTGGATGGCAAACTTAc                                                                                                                             >  2:442238/1‑139 (MQ=255)
             tAACGCCTGACCGGTTGAAAAATTCGCCGCAGGCAGAGCCATTGGAAATACCAGTACGATTATCGCCAGGGGGAACAGCGCAATTAAATACTGCTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCg                                                                                                                        <  1:863406/139‑1 (MQ=255)
             tAACGCCTGACCGGTTGAAAAATTCGCCGCAGGCAGAGCCATTGGAAATACCAGTACGATTATCGCCAGGGGGAACAGCGCAATTAAATACTGCTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCg                                                                                                                        <  2:902277/139‑1 (MQ=255)
               aCGCCTGACCGGTTGAAAAATTCGCCGCAGGCAGAGCCATTGGAAATACCAGTACGATTATCGCCAGGGGGAACAGCGCAATTAAATACTGCTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGcc                                                                                                                      <  1:932220/139‑1 (MQ=255)
                cGCCTGACCGGTTGAAAAATTCGCCGCAGGCAGAGCCATTGGAAATACCAGTACGATTATCGCCAGGGGGAACAGCGCAATTAAATACTGCTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGccc                                                                                                                     >  1:102263/1‑139 (MQ=255)
                      aCCGGTTGAAAAATTCGCCGCAGGCAGAGCCATTGGAAATACCAGTACGATTATCGCCAGGGGGAACAGCGCAATTAAATACTGCTTGATACCAAACAGATTCTTATATTGGATGGCAAACTTACGACCGCCCAACaat                                                                                                               >  1:309244/1‑139 (MQ=255)
                      aCCGGTTGAAAAATTCGCCGCAGGCAGAGCCATTGGAAATACCAGTACGATTATCGCCAGGGGGAACAGCGCAATTAAATACTGCTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGCCcaa                                                                                                                   >  1:118581/1‑135 (MQ=255)
                      aCCGGTTGAAAAATTCGCCGCAGGCAGAGCCATTGGAAATACCAGTACGATTATCGCCAGGGGGAACAGCGCAATTAAATACTGCTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGCCcaa                                                                                                                   <  2:118581/135‑1 (MQ=255)
                      aCCGGTTGAAAAATTCGCCGCAGGCAGAGCCATTGGAAATACCAGTACGATTATCGCCAGGGGGAACAGCGCAATTAAATACTGCTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGCCCAACaat                                                                                                               >  1:162917/1‑139 (MQ=255)
                           ttGAAAAATTCGCCGCAGGCAGAGCCATTGGAAATACCAGTACGATTATCGCCAGGGGGAACAGCGCAATTAAATACTGCTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGCCCAACAATAATGa                                                                                                          >  1:1049985/1‑139 (MQ=255)
                           ttGAAAAATTCGCCGCAGGCAGAGCCATTGGAAATACCAGTACGATTATCGCCAGGGGGAACAGCGCAATTAAATACTGCTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGCCCAACAATAATGa                                                                                                          >  1:262818/1‑139 (MQ=255)
                               aaaaTTCGCCGCAGGCAGAGCCATTGGAAATACCAGTACGATTATCGCCAGGGGGAACAGCGCAATTAAATACTGCTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGCCCAACAATAATGAAAAg                                                                                                      <  2:162917/139‑1 (MQ=255)
                                 aaTTCGCCGCAGGCAGAGCCATTGGAAATACCAGTACGATTATCGCCAGGGGGAACAGCGCAATTAAATACTGCTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGCCCAACAATAATGAAAAGcc                                                                                                    <  2:262818/139‑1 (MQ=255)
                                         gcaggcagAGCCATTGGAAATACCAGTACGATTATCGCCAGGGGGAACAGCGCAATTAAATACTGCTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGCCCAACAATAATGAAAAGCCAACCAGcc                                                                                            <  2:1049985/139‑1 (MQ=255)
                                                gagCCATTGGAAATACCAGTACGATTATCGCCAGGGGGAACAGCGCAATTAAATACTGCTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGCCCAACAATAATGAAAAGCCAACCAGCCCACCGGt                                                                                     <  2:1144024/139‑1 (MQ=255)
                                                gagCCATTGGAAATACCAGTACGATTATCGCCAGGGGGAACAGCGCAATTAAATACTGCTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGCCCAACAATAATGAAAAGCCAACCAGCCCACCGGt                                                                                     <  1:770902/139‑1 (MQ=255)
                                                 agCCATTGGAAATACCAGTACGATTATCGCCAGGGGGAACAGCGCAATTAAATACTGCTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGCCCAACAATAATGAAAAGCCAACCAGCCCACCGGTa                                                                                    <  2:102263/139‑1 (MQ=255)
                                                  gCCATTGGAAATACCAGTACGATTATCGCCAGGGGGAACAGCGCAATTAAATACTGCTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGCCCAACAATAATGAAAAGCCAACCAGCCCACCGGTaa                                                                                   <  1:485415/139‑1 (MQ=255)
                                                       tGGAAATACCAGTACGATTATCGCCAGGGGGAACAGCGCAATTAAATACTGCTTGATACCAAACAGATTCATATATTGGATGGc                                                                                                                                     >  1:1293337/1‑84 (MQ=255)
                                                       tGGAAATACCAGTACGATTATCGCCAGGGGGAACAGCGCAATTAAATACTGCTTGATACCAAACAGATTCATATATTGGATGGc                                                                                                                                     <  2:1293337/84‑1 (MQ=255)
                                                         gAAATACCAGTACGATTATCGCCAGGAGGAACAGCGCAATTAAATACTGCTTGATACCAAACAGATTCATATATTGGATGGCAAACATACCAACGCCCAACAATAATGAAAAGCCAACCAGCCCACCGGTAACAATCAt                                                                            <  1:871220/139‑1 (MQ=255)
                                                               ccAGTACGATTATCGCCAGGGGGAACAGCGCAATTAAATACTGCTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGCCCAACAATAATGAAAAGCCAACCAGCCCACCGGTAACAATCATAATGAt                                                                      <  2:1210828/139‑1 (MQ=255)
                                                                                  ggggAACAGCGCAATTAAATACTGCTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGCCCAACAATAATGAAAAGCCAACCAGCCCACCGGTAACAATCATAATg                                                                        >  1:997111/1‑118 (MQ=255)
                                                                                  ggggAACAGCGCAATTAAATACTGCTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGCCCAACAATAATGAAAAGCCAACCAGCCCACCGGTAACAATCATAATg                                                                        <  2:997111/118‑1 (MQ=255)
                                                                                            gcAATTAAATACTGCTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGCCCAACAATAATGAAAAGCCAACCAGCCCACCGGt                                                                                     <  2:1066195/95‑1 (MQ=255)
                                                                                            gcAATTAAATACTGCTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGCCCAACAATAATGAAAAGCCAACCAGCCCACCGGt                                                                                     >  1:1066195/1‑95 (MQ=255)
                                                                                                     tACTGCTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGCCCAACAATAATGAAAAGCCAAc                                                                                                 >  2:190498/1‑74 (MQ=255)
                                                                                                     tACTGCTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGCCCAACAATAATGAAAAGCCAAc                                                                                                 <  1:190498/74‑1 (MQ=255)
                                                                                                        tGCTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGCCCAACAATAATg                                                                                                           <  1:241639/61‑1 (MQ=255)
                                                                                                        tGCTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGCCCAACAATAATg                                                                                                           >  2:241639/1‑61 (MQ=255)
                                                                                                          cTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGCCcaaca                                                                                                                 >  1:895467/1‑53 (MQ=255)
                                                                                                          cTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGCCcaaca                                                                                                                 <  2:895467/53‑1 (MQ=255)
                                                                                                          cTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGCCCAACAATAATGAAAAGCCAACCAGCCCACCGGTaa                                                                                   <  2:1121109/83‑1 (MQ=255)
                                                                                                          cTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGCCCAACAATAATGAAAAGCCAACCAGCCCACCGGTaa                                                                                   >  1:1121109/1‑83 (MQ=255)
                                                                                                          cTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGCCCAACAATAATGAAAAGCCAACCAGCCCACCGGTAACAATCATAATGATTGAATagag                                                             <  1:292610/105‑1 (MQ=255)
                                                                                                          cTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGCCCAACAATAATGAAAAGCCAACCAGCCCACCGGTAACAATCATAATGATTGAATagag                                                             >  2:292610/1‑105 (MQ=255)
                                                                                                          cTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGCCCAACAATAATGAAAAGCCAACCAGCCCACCGGTAACAATCATAATGATTGAATAGAGCGTATCACGCAtt                                                >  1:314235/1‑118 (MQ=255)
                                                                                                          cTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGCCCAACAATAATGAAAAGCCAACCAGCCCACCGGTAACAATCATAATGATTGAATAGAGCGTATCACGCAtt                                                <  2:314235/118‑1 (MQ=255)
                                                                                                          cTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGCCCAACAATAATGAAAAGCCAACCAGCCCACCGGTAACAATCATAATGATTGAATAGAGCGTATCACGCAt                                                 <  1:283738/117‑1 (MQ=255)
                                                                                                          cTTGATACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGCCCAACAATAATGAAAAGCCAACCAGCCCACCGGTAACAATCATAATGATTGAATAGAGCGTATCACGCAt                                                 >  2:283738/1‑117 (MQ=255)
                                                                                                               tACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGCCCAACAATAATGAAAAGCCAACCAGCCCACCGGTAACAATCATaa                                                                          <  2:10839/87‑1 (MQ=255)
                                                                                                               tACCAAACAGATTCATATATTGGATGGCAAACTTACGACCGCCCAACAATAATGAAAAGCCAACCAGCCCACCGGTAACAATCATaa                                                                          >  1:10839/1‑87 (MQ=255)
                                                                                                                  cAAACAGATTCATATATTGGATGGCAAACTTACGACCGCCCAACAATAATGAAAAGCCAACCAGCCCACCGGTAACAATCATAATGATTGAATAGAGCGTATCACGCATTAGCGTTGGCGCGGCGTCGCCGGTTGCCAt                   >  1:72946/1‑139 (MQ=255)
                                                                                                                    aaCAGATTCATATATTGGATGGCAAACTTACGACCGCCCAACAATAATGAAAAGCCAACCAGCCCACCGGTAACAATCAt                                                                            >  2:916694/1‑80 (MQ=255)
                                                                                                                    aaCAGATTCATATATTGGATGGCAAACTTACGACCGCCCAACAATAATGAAAAGCCAACCAGCCCACCGGTAACAATCAt                                                                            <  1:916694/80‑1 (MQ=255)
                                                                                                                         aTTCATATATTGGATGGCAAACTTACGACCGCCCAACAATAATGAAAAGCCAACGAGCCCACCGGTAACAATCATAATGATTGAATAGAGCGTATCACGCATTAGCGTTGGCGCGGCGTCGCCGGtt                        <  1:799117/127‑1 (MQ=255)
                                                                                                                         aTTCATATATTGGATGGCAAACTTACGACCGCCCAACAATAATGAAAAGCCAACCAGCCCACCGGTAACAATCATAATGa                                                                       <  2:1192536/80‑1 (MQ=255)
                                                                                                                         aTTCATATATTGGATGGCAAACTTACGACCGCCCAACAATAATGAAAAGCCAACCAGCCCACCGGTAACAATCATAATGa                                                                       >  1:1192536/1‑80 (MQ=255)
                                                                                                                         aTTCATATATTGGATGGCAAACTTACGACCGCCCAACAATAATGAAAAGCCAACCAGCCCACCGGTAACAATCATAATGATTGAATAGAGCGTATCACGCATTAGCGTTGGCGCGGCGTCGCCGGtt                        >  2:799117/1‑127 (MQ=255)
                                                                                                                         aTTCATATATTGGATGGCAAACTTACGACCGCCCAACAATAATGAAAAGCCAACCAGCCCACCGGTAACAATCATAATGATTGAATAGAGCGTATCACGCATTAGCGTTGGCGCGGCGTCGCCGGTTGCCATTAAAGCt            >  1:1123581/1‑139 (MQ=255)
                                                                                                                                   tGGATGGCAAACTTACGACCGCCCAACAATAATGAAAAGCCAACCAGCCCACCGGTAACAATCAt                                                                            >  1:1178913/1‑65 (MQ=255)
                                                                                                                                   tGGATGGCAAACTTACGACCGCCCAACAATAATGAAAAGCCAACCAGCCCACCGGTAACAATCATAATGATTGAATAGAGCGTATCACGCATTAGCGTTGGCGCGGCGTCGCCGGTTGCCATTAAAGCTGAAATCAAAc  >  1:10621/1‑139 (MQ=255)
                                                                                                                                   tGGATGGCAAACTTACGACCGCCCAACAATAATGAAAAGCCAACCAGCCCACCGGTAACAATCATAATGATTGAATAGAGCGTATCACGCATTAGCGTTGGCGCGGCGTCGCCGGTTGCCATTAAAGCTGAAATCAAAc  >  2:80138/1‑139 (MQ=255)
                                                                                                                                   tGGATGGCAAACTTACGACCGCCCAACAATAATGAAAAGCCAACCAGCCCACCGGTAACAATCATAATGATTGAATAGAGCGTATCACGCATTAGCGTTGGCGCGGCGTCGCCGGTTGCCATTAAAGCTGAAATCAAAc  >  1:1190037/1‑139 (MQ=255)
                                                                                                                                   tGGATGGCAAACTTACGACCGCCCAACAATAATGAAAAGCCAACCAGCCCACCGGTAACAATCATAATGATTGAATAGAGCGTATCACGCATTAGCGTTGGCGCGGCGTCGCCGGTTGCCATTAAAGCTGAAATCAAAc  >  1:140091/1‑139 (MQ=255)
                                                                                                                                      |                                                                                                                                       
TTAATGCTACCAGTAACGCCTGACCGGTTGAAAAATTCGCCGCAGGCAGAGCCATTGGAAATACCAGTACGATTATCGCCAGGGGGAACAGCGCAATTAAATACTGCTTGATACCAAACAGATTCATATATTGGGTGGCAAACTTACGACCGCCCAACAATAATGAAAAGCCAACCAGCCCACCGGTAACAATCATAATGATTGAATAGAGCGTATCACGCATTAGCGTTGGCGCGGCGTCGCCGGTTGCCATTAAAGCTGAAATCAAAC  >  NC_000913/1271321‑1271590

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A