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
A3 F1 I1 R1 781 46.9 2231650 93.5% 2086592 109.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,761,850 C→T A36T (GCG→ACG)  yibF ← glutathione S‑transferase homolog

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,761,8500CT100.0% 132.1 / NA 41A36T (GCG→ACG) yibFglutathione S‑transferase homolog
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (21/20);  total (21/20)

TTCATTAATTCAATATATTCAGCGATGATCGGCGAATCAAACCAGCATTCGCCCTCTTCGGTCACCAGCACCGGCACTTTTCCTAACGGGTTAAATTGCGCCACGCCGTTGTCCGCGTTATAGGGCAGTTCATTAATAAATTCGAAAGTTATGCCCTTTTCTAACAACAGAATAGAAAGTTTGCGTACAAACGGGCTGGTGTAGCTACCGACGAGTTTCATGCCGAGTCCTTTGTGCGAGGAAAAATAT  >  NC_000913/3761735‑3761983
                                                                                                                   |                                                                                                                                     
ttcattAATTCAATATATTCAGCGATGATCGGCGAATCAAACCAGCATTCGCCCTCTTCGGTCACCAGCACCGGCACTTTTCCTAACGGGTTAAATTGCGCCACGCCGTTGTCCGTGTTATAGGGCAGTTCATtaataa                                                                                                                >  2:971226/1‑139 (MQ=255)
      aaTTCAATATATTCAGCGATGATCGGCGAATCAAACCAGCATTCGCCCTCTTCGGTCACCAGCACCGGCACTTTTCCTAACGGGTTAAATTGCGCCACGCCGTTGTCCGTGTTATAGGGCAGTTCATTAATAAATTCGa                                                                                                          <  1:936792/139‑1 (MQ=255)
                   cAGCGATGATCGGCGAATCAAACCAGCATTCGCCCTCTTCGGTCACCAGCACCGGCACTTTTCCTAACGGGTTAAATTGCGCCACGCCGTTGTCCGTGTTATAGGGCAGTTCATTAATAAATTCGAAAGTTATGCCCtt                                                                                             >  2:331636/1‑139 (MQ=255)
                     gCGATGATCGGCGAATCAAACCAGCATTCGCCCTCTTCGGTCACCAGCACCGGCACTTTTCCTAACGGGTTAAATTGCGCCACGCCGTTGTCCGTGTTATAGGGCAGTTCATTAATAAATTCGAAAGTTATGCCCtttt                                                                                           >  2:46400/1‑139 (MQ=255)
                      cGATGATCGGCGAATCAAACCAGCATTCGCCCTCTTCGGTCACCAGCACCGGCACTTTTCCTAACGGGTTAAATTGCGCCACGCCGTTGTCCGTGTTATAGGGCAGTTCATTAATAAATTCGa                                                                                                          <  1:1059333/123‑1 (MQ=255)
                      cGATGATCGGCGAATCAAACCAGCATTCGCCCTCTTCGGTCACCAGCACCGGCACTTTTCCTAACGGGTTAAATTGCGCCACGCCGTTGTCCGTGTTATAGGGCAGTTCATTAATAAATTCGa                                                                                                          >  2:1059333/1‑123 (MQ=255)
                       gatgatCGGCGAATCAAACCAGCATTCGCCCTCTTCGGTCACCAGCACCGGCACTTTTCCTAACGGGTTAAATTGCGCCACGCCGTTGTCCGTGTTATAGGGCAGTTCATTAATAAATTCGAAAGTTa                                                                                                    <  2:814140/128‑1 (MQ=255)
                       gatgatCGGCGAATCAAACCAGCATTCGCCCTCTTCGGTCACCAGCACCGGCACTTTTCCTAACGGGTTAAATTGCGCCACGCCGTTGTCCGTGTTATAGGGCAGTTCATTAATAAATTCGAAAGTTa                                                                                                    >  1:814140/1‑128 (MQ=255)
                           atCGGCGAATCAAACCAGCATTCGCCCTCTTCGGTCACCAGCACCGGCACTTTTCCTAACGGGTTTAATTGCGCCACGCCGTTGTCCGTGTTATAGGGCAGTTCATTAATAAATTCGAAAGTTATGCCCTTTTCTaaca                                                                                     >  2:146397/1‑139 (MQ=255)
                           atCGGCGAATCAAACCAGCATTCGCCCTCTTCGGTCACCAGCACCGGCACTTTTCCTAACGGGTTAAATTGCGCCACGCCGTTGTCCGTGTTATAGGGCAGTTCATtaat                                                                                                                  <  2:664029/110‑1 (MQ=255)
                           atCGGCGAATCAAACCAGCATTCGCCCTCTTCGGTCACCAGCACCGGCACTTTTCCTAACGGGTTAAATTGCGCCACGCCGTTGTCCGTGTTATAGGGCAGTTCATtaat                                                                                                                  >  1:664029/1‑110 (MQ=255)
                            tCGGCGAATCAAACCAGCATTCGCCCTCTTCGGTCACCAGCACCGGCACTTTTCCTAACGGGTTAAATTGCGCCACGCCGTTGTCCGTGTTATAGGGCAGTTCATTAATAAATTCGAAAGTTATGCCCTTTTCTaacaa                                                                                    <  1:46400/139‑1 (MQ=255)
                                     cAAACCAGCATTCGCCCTCTTCGGTCACCAGCACCGGCACTTTTCCTAACGGGTTAAATTGCGCCACGCCGTTGTCCGTGTTATAggg                                                                                                                              <  1:328309/88‑1 (MQ=255)
                                     cAAACCAGCATTCGCCCTCTTCGGTCACCAGCACCGGCACTTTTCCTAACGGGTTAAATTGCGCCACGCCGTTGTCCGTGTTATAggg                                                                                                                              >  2:328309/1‑88 (MQ=255)
                                               ttCGCCCTCTTCGGTCACCAGCACCGGCACTTTTCCTAACGGGTTAAATTGCGCCACGCCGTTGTCCGTGTTATAGGGCAGTTCATTAATAAATTCGa                                                                                                          <  2:494065/98‑1 (MQ=255)
                                               ttCGCCCTCTTCGGTCACCAGCACCGGCACTTTTCCTAACGGGTTAAATTGCGCCACGCCGTTGTCCGTGTTATAGGGCAGTTCATTAATAAATTCGa                                                                                                          >  1:494065/1‑98 (MQ=255)
                                                  gCCCTCTTCGGTCACCAGCACCGGCACTTTTCCTAACGGGTTAAATTGCGCCACGCCGTTGTCCGTGTTATAGGGCAGTTCATTAATAAATTCGAAAGTTATGCCCTTTTCTAACAACAGAATAGaa                                                                          >  1:1069708/1‑127 (MQ=255)
                                                  gCCCTCTTCGGTCACCAGCACCGGCACTTTTCCTAACGGGTTAAATTGCGCCACGCCGTTGTCCGTGTTATAGGGCAGTTCATTAATAAATTCGAAAGTTATGCCCTTTTCTAACAACAGAATAGaa                                                                          <  2:1069708/127‑1 (MQ=255)
                                                          cGGTCACCAGCACCGGCACTTTTCCTAACGGGTTAAATTGCGCCACGCCGTTGTCCGTGTTATAGGGCAGTTCATTAATAAATTCGAAAGTTATGCCCTTTTCTAACAACAGAATAGAAAGTTTGCGTACAAACGGGCt                                                      <  2:380096/139‑1 (MQ=255)
                                                               aCCAGCACCGGCACTTTTCCTAACGGGTTAAATTGCGCCACGCCGTTGTCCGTGTTATAggg                                                                                                                              <  2:501847/62‑1 (MQ=255)
                                                               aCCAGCACCGGCACTTTTCCTAACGGGTTAAATTGCGCCACGCCGTTGTCCGTGTTATAggg                                                                                                                              >  1:501847/1‑62 (MQ=255)
                                                                         gCACTTTTCCTAACGGGTTAAATTGCGCCACGCCGTTGTCCGTGTTATAGGGCAGTTCATTAATAAATTCGa                                                                                                          >  2:1040123/1‑72 (MQ=255)
                                                                         gCACTTTTCCTAACGGGTTAAATTGCGCCACGCCGTTGTCCGTGTTATAGGGCAGTTCATTAATAAATTCGa                                                                                                          <  1:1040123/72‑1 (MQ=255)
                                                                           aCTTTTCCTAACGGGTTAAATTGCGCCACGCCGTTGTCCGTGTTATAGGGCAGTTCATTAATAAATTCGAAAGTTATGCCCt                                                                                              >  2:401356/1‑82 (MQ=255)
                                                                           aCTTTTCCTAACGGGTTAAATTGCGCCACGCCGTTGTCCGTGTTATAGGGCAGTTCATTAATAAATTCGAAAGTTATGCCCt                                                                                              <  1:401356/82‑1 (MQ=255)
                                                                               ttCCTAACGGGTTAAATTGCGCCACGCCGTTGTCCGTGTTATAGGGCAGTTCATTAATAAATTCGAAAGTTATGCCCTTTTCTAACAACAGAATAGAAAGTTTGCGTACAAACGGGCTGGTGTAGCTACCGACGAGttt                                 >  1:284698/1‑139 (MQ=255)
                                                                                       gggTTAAATTGCGCCACGCCGTTGTCCGTGTTATAGGGCAGTTCATTAATAAATTCGAAAGTTATGCCCTTTTCTAACAACAGAATAGAAAGTTTGCGTACAAACgg                                                         >  2:540847/1‑107 (MQ=255)
                                                                                       gggTTAAATTGCGCCACGCCGTTGTCCGTGTTATAGGGCAGTTCATTAATAAATTCGAAAGTTATGCCCTTTTCTAACAACAGAATAGAAAGTTTGCGTACAAACgg                                                         <  1:540847/107‑1 (MQ=255)
                                                                                       gggTTAAATTGCGCCACGCCGTTGTCCGTGTTATAGGGCAGTTCATTAATAAATTCGAAAGTTATGCCCTTTTCTAACAACAGAATAGAAAGTTTGCGTACAAACGGGCTGGTGTAGCTACCGACGAGTTTCATGCCGa                         <  2:284698/139‑1 (MQ=255)
                                                                                       gggTTAAATTGCGCCACGCCGTTGTCCGTGTTATAGGGCAGTTCATTAATAAATTCGAAAGTTATGCCCTTTTCTAACAACAGAATAGAAAGTTTGCGTACAAACGGGCTGGTGTAGCTACCGACGAGTTTCATGCCGa                         >  1:928539/1‑139 (MQ=255)
                                                                                         gTTAAATTGCGCCACGCCGTTGTCCGTGTTATAGGGCAGTTCATTAATAAATTCGa                                                                                                          <  1:533434/56‑1 (MQ=255)
                                                                                         gTTAAATTGCGCCACGCCGTTGTCCGTGTTATAGGGCAGTTCATTAATAAATTCGa                                                                                                          >  2:533434/1‑56 (MQ=255)
                                                                                          ttAAATTGCGCCACGCCGTTGTCCGTGTTATAGGGCAGTTCATTAATAAATTCGAAAGTTATGCCCTTTTCTAACAACAGAATAGaa                                                                          <  1:998639/87‑1 (MQ=255)
                                                                                          ttAAATTGCGCCACGCCGTTGTCCGTGTTATAGGGCAGTTCATTAATAAATTCGAAAGTTATGCCCTTTTCTAACAACAGAATAGaa                                                                          >  2:998639/1‑87 (MQ=255)
                                                                                          ttAAATTGCGCCACGCCGTTGTCCGTGTTATAGGGCAGTTCATTAATAAATTCGAAAGTTATGCCCTTTTCTAACAACAGAATAGAAAGTTTGCGTACAAACGGGCTGGTGTAGCTACCGACGAGTTTCATGCCGAGTc                      >  1:774814/1‑139 (MQ=255)
                                                                                                   gcCACGCCGTTGTCCGTGTTATAGGGCAGTTCATTAATAAATTCGAAAGTTATGCCCTTTTCTAACAACAGAATAGAAAGTTTGCGTACAAACGGGCTGGTGTAGCTACCGACGAGTTTCATGCCGAGTCCTTTGTGCg             >  2:450601/1‑139 (MQ=255)
                                                                                                   gcCACGCCGTTGTCCGTGTTATAGGGCAGTTCATTAATAAATTCGAAAGTTATGCCCTTTTCTAACAACAGAATAGAAAGTTTGCGTACAAACGGGCTGGTGTAGCTACCGACGAGTTTCATGCCGAGTCCTTTGTGCg             >  2:139122/1‑139 (MQ=255)
                                                                                                      aCGCCGTTGTCCGTGTTATAGGGCAGTTCATTAATAAATTCGAAAGTTATGCCCTTTTCTAACAACAGAATAGAAAGTTTGCGTACAAACGGGCTGGTGTAGCTACCGACGAGTTTCATGCCGAGTCCTTTGTGCGAgg          <  1:146397/139‑1 (MQ=255)
                                                                                                         ccGTTGTCCGTGTTATAGGGCAGTTCATTAATAAATTCGAAAGTTATGCCCTTTTCTAACAACAGAATAGAAAGTTTGCGTACAAACGGGCTGGTGTAGCTACCGACGAGTTTCATGCCGAGTCCTTTGTGCGAGGaaa       <  2:991518/139‑1 (MQ=255)
                                                                                                             tGTCCGTGTTATAGGGCAGTTCATTAATAAATTCGAAAGTTATGCCCTTTTCTAACAACAGAATAGAAAGTTTGCGTACAAACGGGCTGGTGTAGCTACCGACGAGTTTCATGCCGAGTCCTTTGTGCGAGGAAAAata   <  2:774814/139‑1 (MQ=255)
                                                                                                              gTCCGTGTTATAGGGCAGTTCATTAATAAATTCGAAAGTTATGCCCTTTTCTAACAACAGAATAGAAAGTTTGCGTACAAACGGGCTGGTGTAGCTACCGACGAGTTTCATGCCGAGTCCTTTGTGCGAGGAAAAatat  <  1:971226/139‑1 (MQ=255)
                                                                                                                   |                                                                                                                                     
TTCATTAATTCAATATATTCAGCGATGATCGGCGAATCAAACCAGCATTCGCCCTCTTCGGTCACCAGCACCGGCACTTTTCCTAACGGGTTAAATTGCGCCACGCCGTTGTCCGCGTTATAGGGCAGTTCATTAATAAATTCGAAAGTTATGCCCTTTTCTAACAACAGAATAGAAAGTTTGCGTACAAACGGGCTGGTGTAGCTACCGACGAGTTTCATGCCGAGTCCTTTGTGCGAGGAAAAATAT  >  NC_000913/3761735‑3761983

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A