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
A1 F1 I1 R1 315 33.5 1889570 98.7% 1865005 80.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,834,019 C→T V173V (GTG→GTA)  yicI ← alpha‑D‑xyloside xylohydrolase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,834,0190CT100.0% 165.6 / NA 45V173V (GTG→GTA) yicIalpha‑D‑xyloside xylohydrolase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (19/26);  total (19/26)

TATTTTTATACGCCTGTTCAGTACTTGTGCCGCCGTCCCGGTTCCAGGTCTCTACCGTCTGGCCATTGCGCACCAGGGCAGTAAAGCGCTCTCCCAGACCGTAAACTGTTTCGCCAACGCCAAGATCAAGCCGCTCAAACATATAA  >  NC_000913/3833949‑3834094
                                                                      |                                                                           
tatTTTTATACGCCTGTTCAGTACTTGTGCCGCCGTCCCGGTTCCAGGTCTCTACCGTCTGGCCATTGCGTACCAGGGCAg                                                                   >  2:746621/1‑81 (MQ=255)
  tttttATACGCCTGTTCAGTACTTGTGCCGCCGTCCCGGTTCCAGGTCTCTACCGTCTGGCCATTGCGTACCAGGGCAGt                                                                  <  2:746568/80‑1 (MQ=255)
    tttATACGCCTGTTCAGTACTTGTGCCGCCGTCCCGGTTCCAGGTCTCTACCGTCTGGCCATTGCGTACCAGGGCAGTaa                                                                <  1:746569/80‑1 (MQ=255)
        taCGCCTGTTCAGTACTTGTGCCGCCGTCCCGGTTCCAGGTCTCTACCGTCTGGCCATTGCGTACCAGGGCAGTAAAgcgc                                                           >  1:746619/1‑81 (MQ=255)
        taCGCCTGTTCAGTACTTGTGCCGCCGTCCCGGTTCCAGGTCTCTACCGTCTGGCCATTGCGTACCAGGGCAGTAAAgcg                                                            <  2:746570/80‑1 (MQ=255)
         aCGCCTGTTCAGTACTTGTGCCGCCGTCCCGGTTCCAGGTCTCTACCGTCTGGCCATTGCGTACCAGGGCAGTAAAGCGct                                                          >  1:746628/1‑81 (MQ=255)
             cTGTTCAGTACTTGTGCCGCCGTCCCGGTTCCAGGTCTCTACCGTCTGGCCATTGCGTACCAGGGCAGTAAAGCGCTCTcc                                                      <  2:746571/81‑1 (MQ=255)
                ttCAGTACTTGTGCCGCCGTCCCGGTTCCAGGTCTCTACCGTCTGGCCATTGCGTACCAGGGCAGTAAAGCGCTCTCCCAg                                                   <  1:746572/81‑1 (MQ=255)
                  cAGTACTTGTGCCGCCGTCCCGGTTCCAGGTCTCTACCGTCTGGCCATTGCGTACCAGGGCAGTAAAGCGCTCTCCCAGAc                                                 >  2:746639/1‑81 (MQ=255)
                   aGTACTTGTGCCGCCGTCCCGGTTCCAGGTCTCTACCGTCTGGCCATTGCGTACCAGGGCAGTAAAGCGCTCTCCCAGAcc                                                <  2:746574/81‑1 (MQ=255)
                   aGTACTTGTGCCGCCGTCCCGGTTCCAGGTCTCTACCGTCTGGCCATTGCGTACCAGGGCAGTAAAGCGCTCTCCCAGAcc                                                <  1:746573/81‑1 (MQ=255)
                     tACTTGTGCCGCCGTCCCGGTTCCAGGTCTCTACCGTCTGGCCATTGCGTACCAGGGCAGTAAAGCGCTCTCCCAGACCg                                               >  2:746622/1‑80 (MQ=255)
                      aCTTGTGCCGCCGTCCCGGTTCCAGGTCTCTACCGTCTGGCCATTGCGTACCAGGGCAGTAAAGCGCTCTCCCAGACCGt                                              >  2:746617/1‑80 (MQ=255)
                       cTTGTGCCGCCGTCCCGGTTCCAGGTCTCTACCGTCTGGCCATTGCGTACCAGGGCAGTAAAGCGCTCTCCCAGACCGTa                                             <  2:746575/80‑1 (MQ=255)
                          gtgCCGCCGTCCCGGTTCCAGGTCTCTACCGTCTGGCCATTGCGTACCAGGGCAGTAAAGCGCTCTCCCAGACCGTAAAc                                          <  1:746576/80‑1 (MQ=255)
                          gtgCCGCCGTCCCGGTTCCAGGTCTCTACCGTCTGGCCATTGCGTACCAGGGCAGTAAAGCGCTCTCCCAGACCGTAAACt                                         >  2:746635/1‑81 (MQ=255)
                           tgCCGCCGTCCCGGTTCCAGGTCTCTACCGTCTGGCCATTGCGTACCAGGGCAGTAAAGCGCTCTCCCAGACCGTAAACTg                                        <  1:746577/81‑1 (MQ=255)
                              cgccgTCCCGGTTCCAGGTCTCTACCGTCTGGCCATTGCGTACCAGGGCAGTAAAGCGCTCTCCCAGACCGTAAACTGttt                                     <  1:746578/81‑1 (MQ=255)
                               gccgTCCCGGTTCCAGGTCTCTACCGTCTGGCCATTGCGTACCAGGGCAGTAAAGCGCTCTCCCAGACCGTAAACTGTTTc                                    <  1:746580/81‑1 (MQ=255)
                               gccgTCCCGGTTCCAGGTCTCTACCGTCTGGCCATTGCGTACCAGGGCAGTAAAGCGCTCTCCCAGACCGTAAACTGTTTc                                    <  2:746579/81‑1 (MQ=255)
                               gccgTCCCGGTTCCAGGTCTCTACCGTCTGGCCATTGCGTACCAGGGCAGTAAAGCGCTCTCCCAGACCGTAAACTGTTTc                                    >  1:746637/1‑81 (MQ=255)
                               gccgTCCCGGTTCCAGGTCTCTACCGTCTGGCCATTGCGTACCAGGGCAGTAAAGCGCTCTCCCAGACCGTAAACTGTTTc                                    >  1:746633/1‑81 (MQ=255)
                               gccgTCCCGGTTCCAGGTCTCTACCGTCTGGCCATTGCGTACCAGGGCAGTAAAGCGCTCTCCCAGACCGTAAACTGTTTc                                    <  1:746581/81‑1 (MQ=255)
                                ccgTCCCGGTTCCAGGTCTCTACCGTCTGGCCATTGCGTACCAGGGCAGTAAAGCGCTCTCCCAGACCGTAAACTGTTTcg                                   <  2:746583/81‑1 (MQ=255)
                                ccgTCCCGGTTCCAGGTCTCTACCGTCTGGCCATTGCGTACCAGGGCAGTAAAGCGCTCTCCCAGACCGTAAACTGTTTcg                                   <  1:746582/81‑1 (MQ=255)
                                 cgTCCCGGTTCCAGGTCTCTACCGTCTGGCCATTGCGTACCAGGGCAGTAAAGCGCTCTCCCAGACCGTAAACTGTTTcgc                                  >  2:746632/1‑81 (MQ=255)
                                  gTCCCGGTTCCAGGTCTCTACCGTCTGGCCATTGCGTACCAGGGCAGTAAAGCGCTCTCCCAGACCGTAAACTGTTTcgcc                                 <  1:746584/81‑1 (MQ=255)
                                  gTCCCGGTTCCAGGTCTCTACCGTCTGGCCATTGCGTACCAGGGCAGTAAAGCGCTCTCCCAGACCGTAAACTGTTTcgc                                  >  1:746615/1‑80 (MQ=255)
                                      cGGTTCCAGGTCTCTACCGTCTGGCCATTGCGTACCAGGGCAGTAAAGCGCTCTCCCAGACCGTAAACTGTTTcgccaacg                             <  2:746585/81‑1 (MQ=255)
                                       ggTTCCAGGTCTCTACCGTCTGGCCATTGCGTACCAGGGCAGTAAAGCGCTCTCCCAGACCGTAAACTGTTTcgccaacgc                            <  2:746586/81‑1 (MQ=255)
                                       ggTTCCAGGTCTCTACCGTCTGGCCATTGCGTACCAGGGCAGTAAAGCGCTCTCCCAGACCGTAAACTGTTTcgccaacgc                            >  1:746626/1‑81 (MQ=255)
                                       ggTTCCAGGTCTCTACCGTCTGGCCATTGCGTACCAGGGCAGTAAAGCGCTCTCCCAGACCGTAAACTGTTTcgccaacgc                            >  2:746625/1‑81 (MQ=255)
                                        gTTCCAGGTCTCTACCGTCTGGCCATTGCGTACCAGGGCAGTAAAGCGCTCTCCCAGACCGTAAACTGTTTcgccaacgcc                           <  1:746587/81‑1 (MQ=255)
                                         ttCCAGGTCTCTACCGTCTGGCCATTGCGTACCAGGGCAGTAAAGCGCTCTCCCAGACCGTAAACTGTTTcgccaacgcca                          <  1:746588/81‑1 (MQ=255)
                                           ccAGGTCTCTACCGTCTGGCCATTGCGTACCAGGGCAGTAAAGCGCTCTCCCAGACCGTAAACTGTTTcgccaacgcc                           >  2:746623/1‑78 (MQ=255)
                                            cAGGTCTCTACCGTCTGGCCATTGCGTACCAGGGCAGTAAAGCGCTCTCCCAGACCGTAAACTGTTTcgccaacgcc                           >  2:746630/1‑77 (MQ=255)
                                             aGGTCTCTACCGTCTGGCCATTGCGTACCAGGGCAGTAAAGCGCTCTCCCAGACCGTAAACTGTTTcgccaacgcc                           >  2:746650/1‑76 (MQ=255)
                                              ggTCTCTACCGTCTGGCCATTGCGTACCAGGGCAGTAAAGCGCTCTCCCAGACCGTAAACTGTTTCGCCAACGCCAAGATc                     <  2:746589/81‑1 (MQ=255)
                                                 ctctACCGTCTGGCCATTGCGTACCAGGGCAGTAAAGCGCTCTCCCAGACCGTAAACTGTTTCGCCAACGCCAAGATCAAg                  >  1:746634/1‑81 (MQ=255)
                                                    tACCGTCTGGCCATTGCGTACCAGGGCAGTAAAGCGCTCTCCCAGACCGTAAACTGTTTCGCCAACGCCAAGATCAAg                  <  1:746590/78‑1 (MQ=255)
                                                      ccGTCTGGCCATTGCGTACCAGGGCAGTAAAGCGCTCTCCCAGACCGTAAACTGTTTCGCCAACGCCAAGATCAAGCCg               <  2:746591/79‑1 (MQ=255)
                                                          cTGGCCATTGCGTACCAGGGCAGTAAAGCGCTCTCCCAGACCGTAAACTGTTTCGCCAACGCCAAGATCAAGCCGCTCaaa         >  2:746643/1‑81 (MQ=255)
                                                             gCCATTGCGTACCAGGGCAGTAAAGCGCTCTCCCAGACCGTAAACTGTTTCGCCAACGCCAAGATCAAGCCGCTCAAACat      <  1:746592/81‑1 (MQ=255)
                                                                aTTGCGTACCAGGGCAGTAAAGCGCTCTCCCAGACCGTAAACTGTTTCGCCAACGCCAAGATCAAGCCGCTCAAACatat    >  1:746644/1‑80 (MQ=255)
                                                                 ttGCGTACCAGGGCAGTAAAGCGCTCTCCCAGACCGTAAACTGTTTCGCCAACGCCAAGATCAAGCCGCTCAAACATATaa  <  2:746593/81‑1 (MQ=255)
                                                                      |                                                                           
TATTTTTATACGCCTGTTCAGTACTTGTGCCGCCGTCCCGGTTCCAGGTCTCTACCGTCTGGCCATTGCGCACCAGGGCAGTAAAGCGCTCTCCCAGACCGTAAACTGTTTCGCCAACGCCAAGATCAAGCCGCTCAAACATATAA  >  NC_000913/3833949‑3834094

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

GATK/CNVnator alignment

N/A