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
A4 F28 I3 R2 52 92.4 4932871 87.1% 4296530 63.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA minE 1,419,579 G→A R128R (CGC→CGT)  ccmH ← heme lyase, CcmH subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,419,5790GA96.3% 82.6 / ‑6.0 27R128R (CGC→CGT) ccmHheme lyase, CcmH subunit
Reads supporting (aligned to +/- strand):  ref base G (0/0);  major base A (2/24);  minor base T (0/1);  total (2/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACATATCCGGCACGCTTACCTTCCGGCACGCTTTGTTCAGGAAACGCTTCCGGCACCACGCGTACCCGACGCCGCGAGCGGGCGTATATGACCCAACCGCCAATGCCAATAGCCACTACTGGC  >  minE/1419520‑1419642
                                                           |                                                               
acaTATCCGGCACGCTTACCTTCCGGCACGCTTTGTTCAGGAAACGCTTCCGGCACCACACGTACCCGAcg                                                      >  1:3284092/1‑71 (MQ=255)
acaTATCCGGCACGCTTACCTTCCGGCACGCTTTGTTCAGGAAACGCTTCCGGCACCACACGTACCCGAcg                                                      >  1:1966946/1‑71 (MQ=255)
     tCCGGCACGCTTACCTTCCGGCACGCTTTGTTCAGGAAACGCTTCCGGCACCACACGTACCCGAcgccgc                                                  <  1:343129/70‑1 (MQ=255)
     tCCGGCACGCTTACCTTCCGGCACGCTTTGTTCAGGAAACGCTTCCGGCACCACACGTACCCGAcgccgc                                                  <  1:1748646/70‑1 (MQ=255)
     tCCGGCACGCTTACCTTCCGGCACGCTTTGTTCAGGAAACGCTTCCGGCACCACACGTACCCGAcgccgc                                                  <  1:2716645/70‑1 (MQ=255)
     tCCGGCACGCTTACCTTCCGGCACGCTTTGTTCAGGAAACGCTTCCGGCACCACACGTACCCGACGCcgcg                                                 <  1:654834/71‑1 (MQ=255)
     tCCGGCACGCTTACCTTCCGGCACGCTTTGTTCAGGAAACGCTTCCGGCACCACACGTACCCGACGCcgcg                                                 <  1:1575999/71‑1 (MQ=255)
        ggCACTCTTACCTTCCGGCACGCTTTGTTCATGAAACGCTTCCGGCACCACTCGTACCCGACGCCGCGAGc                                              <  1:3182626/71‑1 (MQ=255)
        ggCACGCTTACCTTCCGGCACGCTTTGTTCAGGAAACGCTTCCGGCACCACACGTACCCGACGCCGCGAGc                                              <  1:268206/71‑1 (MQ=255)
        ggCACGCTTACCTTCCGGCACGCTTTGTTCAGGAAACGCTTCCGGCACCACACGTACCCGACGCCGCGAGc                                              <  1:4200238/71‑1 (MQ=255)
        ggCACGCTTACCTTCCGGCACGCTTTGTTCAGGAAACGCTTCCGGCACCACACGTACCCGACGCCGCGAGc                                              <  1:2128468/71‑1 (MQ=255)
        ggCACGCTTACCTTCCGGCACGCTTTGTTCAGGAAACGCTTCCGGCACCACACGTACCCGACGCCGCGAGc                                              <  1:1772476/71‑1 (MQ=255)
                      ccGGCACGCTTTGTTCAGGAAACGCTTCCGGCACCACACGTACCCGACGCCGCGAGCGGGCGTATATGa                                  <  1:2571600/69‑1 (MQ=255)
                      ccGGCACGCTTTGTTCAGGAAACGCTTCCGGCACCACACGTACCCGACGCCGCGAGCGGGCGTATATGa                                  <  1:2067630/69‑1 (MQ=255)
                      ccGGCACGCTTTGTTCAGGAAACGCTTCCGGCACCACACGTACCCGACGCCGCGAGCGGGCGTATATGa                                  <  1:3580105/69‑1 (MQ=255)
                      ccGGCACGCTTTGTTCAGGAAACGCTTCCGGCACCACACGTACCCGACGCCGCGAGCGGGCGTATATGa                                  <  1:4154495/69‑1 (MQ=255)
                       cGGCACGCTTTGTTCAGGAAACGCTTCCGGCACCACACGTACCCGACGCCGCGAGCGGGCGTATATGa                                  <  1:1371547/68‑1 (MQ=255)
                               tttGTTCAGGAAACGCTTCCGGCACCACACGTACCCGACGCCGCGAGCGGGCGTATATGACCCAACCgcc                        <  1:1389518/70‑1 (MQ=255)
                                   ttCAGGAAACGCTTCCGGCACCACACGTACCCGACGCCGCGAGCGGGCGTATATGACCCAACCgccaatgc                   <  1:2753304/71‑1 (MQ=255)
                                     cAGGAAACGCTTCCGGCACCACACGTACCCGACGCCGCGAGCGGGCGTATATGACCCAACCgccaatgcc                  <  1:4738303/70‑1 (MQ=255)
                                          aaCGCTTCCGGCACCACACGTACCCGACGCCGCGAGCGGGCGTATATGACCCAACCGCCAATGCCAATAGc            <  1:4812262/71‑1 (MQ=255)
                                          aaCGCTTCCGGCACCACACGTACCCGACGCCGCGAGCGGGCGTATATGACCCAACCGCCAATGCCAATAGc            <  1:3179140/71‑1 (MQ=255)
                                          aaCGCTTCCGGCACCACACGTACCCGACGCCGCGAGCGGGCGTATATGACCCAACCGCCAATGCCAATAGc            <  1:1717461/71‑1 (MQ=255)
                                             gCTTCCGGCACCACACGTACCCGACGCCGCGAGCGGGCGTATATGACCCAACCGCCAATGCCAATAGCCac         <  1:462725/71‑1 (MQ=255)
                                                    gCACCACACGTACCCGACGCCGCGAGCGGGCGTATATGACCCAACCGCCAATGCCAATAGCCACTACTGgc  <  1:1199655/71‑1 (MQ=255)
                                                    gCACCACACGTACCCGACGCCGCGAGCGGGCGTATATGACCCAACCGCCAATGCCAATAGCCACTACTGgc  <  1:1162317/71‑1 (MQ=255)
                                                    gCACCACACGTACCCGACGCCGCGAGCGGGCGTATATGACCCAACCGCCAATGCCAATAGCCACTACTGgc  <  1:2503516/71‑1 (MQ=255)
                                                           |                                                               
ACATATCCGGCACGCTTACCTTCCGGCACGCTTTGTTCAGGAAACGCTTCCGGCACCACGCGTACCCGACGCCGCGAGCGGGCGTATATGACCCAACCGCCAATGCCAATAGCCACTACTGGC  >  minE/1419520‑1419642

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A