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 I2 R1 765 46.1 2269152 93.8% 2128464 105.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,096,673 G→A *97* (TAG→TAA)  yggU → UPF0235 family protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,096,6730GA100.0% 41.1 / NA 14*97* (TAG→TAA) yggUUPF0235 family protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (6/8);  total (6/8)

CTCGGTAAGCAATTCCGGGTTGCCAAAAGCCAGGTGGTGATTGAAAAAGGCGAACTTGGCCGCCACAAACAAATTAAAATCATTAATCCGCAACAAATCCCGCCAGAAATCGCGGCGTTAATTAATTAGGTATCCTATGCAAAAAGTTGTCCTCGCAACCGGCAATGTCGGTAAAGTGCGTGAGCTGGCGTCGCTGCTTAGCGACTTCGGTCTTGATATC  >  NC_000913/3096545‑3096764
                                                                                                                                |                                                                                           
ctcGGTAAGCAATTCCGGGTTGCCAAAAGCCAGGTGGTGATTGAAAAAGGCGAACTTGGCCGCCACAAACAAATTAAAATCATTAATCCGCAACAAATCCCGCCAGAAATCGCGGCGTTAATTAATTAAGTATCCTATg                                                                                   >  2:997360/1‑139 (MQ=255)
 tcGGTAAGCAATTCCGGGTTGCCAAAAGCCAGGTGGTGATTGAAAAAGGCGAACTTGGCCGCCACAAACAAATTAAAATCATTAATCCGCAACAAATCCCGCCAGAAATCGCGGCGTTAATTAATTAAGTATCCTATGc                                                                                  >  2:1090393/1‑139 (MQ=255)
                 ggTTGCCAAAAGCCAGGTGGTGATTGAAAAAGGCGAACTTGGCCGCCACAAACAAATTAAAATCATTAATCCGCAACAAATCCCGCCAGAAATCGCGGCGTTAATTAATTAAGTATCCTATGCAAAAAg                                                                            <  1:589708/129‑1 (MQ=255)
                 ggTTGCCAAAAGCCAGGTGGTGATTGAAAAAGGCGAACTTGGCCGCCACAAACAAATTAAAATCATTAATCCGCAACAAATCCCGCCAGAAATCGCGGCGTTAATTAATTAAGTATCCTATGCAAAAAg                                                                            >  2:589708/1‑129 (MQ=255)
                            gCCAGGTGGTGATTGAAAAAGGCGAACTTGGCCGCCACAAACAAATTAAAATCATTAATCCGCAACAAATCCCGCCAGAAATCGCGGCGTTAATTAATTAAGTATCCTATGCAAAAAGTTGTCCTCGCAACCGGCAATg                                                       <  2:702304/139‑1 (MQ=255)
                                                                   aacaaaTTAAAATCATTAATCCGCAACAAATCCCGCCAGAAATCGCGGCGTTAATTAATTAAGTATCCTATGCAAAAAGTTGTCCTCGCAACCGGCAATGTCGGTAAAGTGCGTGAGCTGGCGTCGCTGCTTAGCGACt                <  2:97200/139‑1 (MQ=255)
                                                                                 aTTAATCCGCAACAAATCCCGCCAGAAATCGCGGCGTTAATTAATTAAGTATCCTATGCAAAAAGTTGTCCTCGCAACCGGCAATGTCGGTAAAGTGCGTGAGCTGGCGTCGCTGCTTAGCGACTTCGGTCTTGATATc  <  1:146954/139‑1 (MQ=255)
                                                                                 aTTAATCCGCAACAAATCCCGCCAGAAATCGCGGCGTTAATTAATTAAGTATCCTATGCAAAAAGTTGTCCTCGCAACCGGCAATGTCGGTAAAGTGCGTGAGCTGGCGTCGCTGCTTAGCGACTTCGGTCTTGATATc  <  1:997360/139‑1 (MQ=255)
                                                                                  ttAATCCGCAACAAATCCCGCCAGAAATCGCGGCGTTAATTAATTAAGTATCCt                                                                                      >  1:288665/1‑54 (MQ=255)
                                                                                  ttAATCCGCAACAAATCCCGCCAGAAATCGCGGCGTTAATTAATTAAGTATCCt                                                                                      <  2:288665/54‑1 (MQ=255)
                                                                                                                cggcgTTAATTAATTAAGTATCCTATGCAAAAAGTTGTCCTCGCAACCGGCaa                                                         >  1:1098433/1‑53 (MQ=255)
                                                                                                                cggcgTTAATTAATTAAGTATCCTATGCAAAAAGTTGTCCTCGCAACCGGCaa                                                         <  2:1098433/53‑1 (MQ=255)
                                                                                                                cggcgTTAATTAATTAAGTATCCTATGCAAAAAGTTGTCCTCGCAACCGGCAATGTCg                                                    >  1:162269/1‑58 (MQ=255)
                                                                                                                cggcgTTAATTAATTAAGTATCCTATGCAAAAAGTTGTCCTCGCAACCGGCAATGTCg                                                    <  2:162269/58‑1 (MQ=255)
                                                                                                                                |                                                                                           
CTCGGTAAGCAATTCCGGGTTGCCAAAAGCCAGGTGGTGATTGAAAAAGGCGAACTTGGCCGCCACAAACAAATTAAAATCATTAATCCGCAACAAATCCCGCCAGAAATCGCGGCGTTAATTAATTAGGTATCCTATGCAAAAAGTTGTCCTCGCAACCGGCAATGTCGGTAAAGTGCGTGAGCTGGCGTCGCTGCTTAGCGACTTCGGTCTTGATATC  >  NC_000913/3096545‑3096764

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ 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