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
A6 F1 I1 R1 750 51.0 2595496 93.6% 2429384 106.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,619,957 G→A *128* (TAG→TAA)  marA → multiple antibiotic resistance transcriptional regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,619,9570GA100.0% 43.6 / NA 15*128* (TAG→TAA) marAmultiple antibiotic resistance transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (8/7);  total (8/7)

AGTCGCAACAAACTCTGACCCGAACCTTCAAAAATTACTTTGATGTTCCGCCGCATAAATACCGGATGACCAATATGCAGGGCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAGTTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCTTTTCCGCGCAGGGCGTTGCGGAACAAACCACGCAGCC  >  NC_000913/1619833‑1620068
                                                                                                                            |                                                                                                               
aGTCGCAACAAACTCTGACCCGAACCTTCAAAAATTACTTTGATGTTCCGCCGCATAAATACCGGATGACCAATATGCAGGGCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACa                                                                                                   >  1:988118/1‑139 (MQ=255)
                      aaCCTTCAAAAATTACTTTGATGTTCCGCCGCATAAATACCGGATGACCAATATGCAGGGCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGaa                                                                             >  2:1201343/1‑139 (MQ=255)
                                                     cATAAATACCGGATGACCAATATGCAGGGCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCtt                                              <  2:1006709/139‑1 (MQ=255)
                                                                         tatGCAGGGCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCTTTTCCGCGCAggg                          <  1:213884/139‑1 (MQ=255)
                                                                              aGGGCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGaa                                                                                                            >  1:892777/1‑52 (MQ=255)
                                                                              aGGGCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGaa                                                                                                            <  2:892777/52‑1 (MQ=255)
                                                                               gggCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCTTTTCCGCGCAGGGCGTTGc                    >  1:1248292/1‑139 (MQ=255)
                                                                                     aTCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGAc                                                                                                    >  1:829752/1‑53 (MQ=255)
                                                                                     aTCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGAc                                                                                                    <  2:829752/53‑1 (MQ=255)
                                                                                     aTCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCTTTTCCGCGCAGGGCGTTGCGGAACa              >  2:629265/1‑139 (MQ=255)
                                                                                                 aCATCCATTAAATCATTACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCTTTTCCGCGCAGGGCGTTGCGGAACAAACCACGCAGcc  <  2:988118/139‑1 (MQ=255)
                                                                                                                ttACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTc                                                                    >  1:120457/1‑58 (MQ=255)
                                                                                                                ttACAACAGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTc                                                                    <  2:120457/58‑1 (MQ=255)
                                                                                                                  acaacaGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCTTTTCCGCGCAGGGCGTTGCGGAACAAACCACGCAGcc  >  1:215071/1‑122 (MQ=255)
                                                                                                                  acaacaGCTAATTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCTTTTCCGCGCAGGGCGTTGCGGAACAAACCACGCAGcc  <  2:215071/122‑1 (MQ=255)
                                                                                                                            |                                                                                                               
AGTCGCAACAAACTCTGACCCGAACCTTCAAAAATTACTTTGATGTTCCGCCGCATAAATACCGGATGACCAATATGCAGGGCGAATCGCGCTTTTTACATCCATTAAATCATTACAACAGCTAGTTGAAAACGTGACAACGTCACTGAGGCAATCATGAAACCACTTTCATCCGCAATAGCAGCTGCGCTTATTCTCTTTTCCGCGCAGGGCGTTGCGGAACAAACCACGCAGCC  >  NC_000913/1619833‑1620068

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A