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
A5 F58 I1 R1 20 92.2 2125266 63.9% 1358044 150.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA CP000730 2,337,959 C→T intergenic (‑125/‑119) adhR ← / → USA300HOU_2196 possible MerR family transcriptional regulator/hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007302,337,9590CT100.0% 24.8 / NA 8intergenic (‑125/‑119)adhR/USA300HOU_2196possible MerR family transcriptional regulator/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (5/3);  total (5/3)

CTTCTTTAGTTTTCATTGCGACTATCCTTTCAGTTATGTTTGGTCGTCTAAAGTAATGTTGCTTTATATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTACATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAGATTGATAATATTTAATTTTTTGAAAATTATTTTAGTTGCAATTTTTGGGTGATGCGGAAAATTTGGGTGATC  >  CP000730/2337819‑2338098
                                                                                                                                            |                                                                                                                                           
cttcttTAGTTTTCATTGCGACTATCCTTTCAGTTATGTTTGGTCGTCTAAAGTAATGTTGCTTTATATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTATATTTCATCg                                                                                                                                    >  2:816467/1‑150 (MQ=255)
cttcttTAGTTTTCATTGCGACTATCCTTTCAGTTATGTTTGGTCGTCTAAAGTAATGTTGCTTTATATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTATATTTCATCg                                                                                                                                    <  1:816467/150‑1 (MQ=255)
     ttAGTTTTCATTGCGACTATCCTTTCAGTTATGTTTGGTCGTCTAAAGTAATGTTGCTTTATATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTATATTTCATCGTTTTTa                                                                                                                              <  2:1048624/151‑1 (MQ=255)
              aTTGCGACTATCCTTTCAGTTATGTTTGGTCGTCTAAAGTAATGTTGCTTTATATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTATATTTCATCGTTTTTAATTACTTTa                                                                                                                     >  1:455151/1‑151 (MQ=255)
                                                         gTTGCTTTATATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAg                                                                          >  2:730096/1‑151 (MQ=255)
                                                                     atTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTATATTTCATCGTTTTTAATTACTTTTAAAATTTTATAACTTAATTCTTTAAAATTATATAATCATTAAGATTTATTAtttt                                                              >  2:557904/1‑151 (MQ=255)
                                                                                                                 taaatttGTCTCTTTTTTAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAGATTGATAATATTTAATTTTTTGAAAATTATTTTAGTTGCAATTTTTGGGTGATGCg                  >  1:529530/1‑151 (MQ=255)
                                                                                                                                 ttAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAGATTGATAATATTTAATTTTTTGAAAATTATTTTAGTTGCAATTTTTGGGTGATGCGGAAAATTTGGGTGATc  <  1:557904/151‑1 (MQ=255)
                                                                                                                                            |                                                                                                                                           
CTTCTTTAGTTTTCATTGCGACTATCCTTTCAGTTATGTTTGGTCGTCTAAAGTAATGTTGCTTTATATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTACATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAGATTGATAATATTTAATTTTTTGAAAATTATTTTAGTTGCAATTTTTGGGTGATGCGGAAAATTTGGGTGATC  >  CP000730/2337819‑2338098

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A