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
A9 F1 I2 R1 78 48.0 2243616 94.8% 2126947 114.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,863,165 T→C R277R (CGT→CGC)  ygbK → FliA‑regulated DUF1537 family protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,863,1650TC100.0% 66.9 / NA 19R277R (CGT→CGC) ygbKFliA‑regulated DUF1537 family protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (13/6);  total (13/6)

AAACGGTAACCAGGCTCGCAAAGCAGGGCGTCCGCTCGCTGGGCGCGGCGTAGTGCTCTCCGGTTCATGCTCTCAAATGACCAACCGCCAGGTAGCACATTACCGTCAAATTGCACCAGCCCGTGAAGTTGATGTGGCACGCTGCCTCTCAATTGAAACTCTGGCCGCTTATGCACACGAACTGGCAGAGTGGGTTCTGGGCCAGGAAAGTGTACTTGCTCCACTGGTTTTTGCCACCGCCAGCACTGA  >  NC_000913/2863042‑2863290
                                                                                                                           |                                                                                                                             
aaaCGGTAACCAGGCTCGCAAAGCAGGGCGTCCGCTCGCTGGGCGCGGCGTAGTGCTCTCCGGTTCATGCTCTCAAATGACCAACCGCCAGGTAGCACATTACCGTCAAATTGCACCAGCCCGCGAAGTTGATGTGGCa                                                                                                                <  2:248576/139‑1 (MQ=255)
             gCTCGCAAAGCAGGGCGTCCGCTCGCTGGGCGCGGCGTAGTGCTCTCCGGTTCATGCTCTCAAATGACCAACCGCCAGGTAGCACATTACCGTCAAATTGCACCAGCCCGCGAAGTTGATGTGGCACGCTGCCTCTCaa                                                                                                   >  1:313491/1‑139 (MQ=255)
                          ggCGTCCGCTCGCTGGGCGCGGCGTAGTGCTCTCCGGTTCATGCTCTCAAATGACCAACCGCCAGGTAGCACATTACCGTCAAATTGCACCAGCCCGCGAAGTTGATGTGGCACGCTGCCTCTCAATTGAAACTCTGGc                                                                                      <  2:589586/139‑1 (MQ=255)
                                 gctcgctGGGCGCGGCGTAGTGCTCTCCGGTTCATGCTCTCAAATGACCAACCGCCAGGTAGCACATTACCGTCAAATTGCACCAGCCCGCGAAGTTGATGTGGCACGCTGCCTCTCAATTGAAACTCTGGCCGCTTAt                                                                               >  1:578501/1‑139 (MQ=255)
                                    cgctGGGCGCGGCGTAGTGCTCTCCGGTTCATGCTCTCAAATGACCAACCGCCAGGTAGCACATTACCGTCAAATTGCACCAGCCCGCGAAGTTGATGTGGCACGCTGCCTCTCAATTGAAACTCTGGCCGCTTATGca                                                                            >  2:1005804/1‑139 (MQ=255)
                                      ctGGGCGCGGCGTAGTGCTCTCCGGTTCATGCTCTCAAATGACCAACCGCCAGGTAGCACATTACCGTCAAATTGCACCAGCCCGCGAAGTTGATGTGGCACGCTGCCTCTCAATTGAAACTCTGGCCGCTTATGcaca                                                                          <  1:1005804/139‑1 (MQ=255)
                                                          tcCGGTTCATGCTCTCAAATGACCAACCGCCAGGTAGCACATTACCGTCAAATTGCACCAGCCCGCGAAGTTGATGTGGCACGCTGCCTCTCAATTGAAACTCTGGCCGCTTATGCACACGAACTGGCAGAGTGGGTTc                                                      >  1:536027/1‑139 (MQ=255)
                                                               ttCATGCTCTCAAATGACCAACCGCCAGGTAGCACATTACCGTCAAATTGCACCAGCCCGCGAAGTTGATGTGGCACGCTGCCTCTCAATTGAAACTCTGGCCGCTTATGCACACGaa                                                                      <  2:442985/118‑1 (MQ=255)
                                                               ttCATGCTCTCAAATGACCAACCGCCAGGTAGCACATTACCGTCAAATTGCACCAGCCCGCGAAGTTGATGTGGCACGCTGCCTCTCAATTGAAACTCTGGCCGCTTATGCACACGaa                                                                      >  1:442985/1‑118 (MQ=255)
                                                                 cATGCTCTCAAATGACCAACCGCCAGGTAGCACATTACCGTCAAATTGCACCAGCCCGCGAAGTTGATGTGGCACGCTGCCTCTCAATTGAAACTCTGGCCGCTTATGCACACGAACTGGCAGAGTGGGTTCTGGGCCa                                               >  2:878319/1‑139 (MQ=255)
                                                                   tGCTCTCAAATGACCAACCGCCAGGTAGCACATTACCGTCAAATTGCACCAGCCCGCGAAg                                                                                                                           >  1:694918/1‑61 (MQ=255)
                                                                   tGCTCTCAAATGACCAACCGCCAGGTAGCACAGTACCGTCAAATTGCACCAGCCCGCGAAg                                                                                                                           <  2:694918/61‑1 (MQ=255)
                                                                      tctcAAATGACCAACCGCCAGGTAGCACATTACCGTCAAATTGCACCAGCCCGCGAAGTTGATGTGGCACGCTGCCTCTCAATTGAAACTCTGGCCGCTTATGCACACGAACTGGCAGAGTGGGTTCTGGGCCAGGaaa                                          >  1:42477/1‑139 (MQ=255)
                                                                             tGACCAACCGCCAGGTAGCACATTACCGTCAAATTGCACCAGCCCGCGAAGTTGATGTGGCACGCTGCCTCTCAATTGAAACTCTGGCCGCTTATGCACACGAACTGGCAGAGTGGGTTCTGGGCCAGGAAAGTGTACt                                   <  2:663567/139‑1 (MQ=255)
                                                                                  aaCCGCCAGGTAGCACATTACCGTCAAATTGCACCAGCCCGCGAAGTTGATGTGGCACGCTGCCTCTCAATTGAAACTCTGGCCGCTTATGCACACGAACTGGCAGAGTGGGTTCTGGGCCAGGGAAGTGTACTTGCTc                              >  1:580467/1‑139 (MQ=255)
                                                                                  aaCCGCCAGGTAGCACATTACCGTCAAATTGCACCAGCCCGCGAAGTTGATGTGGCACGCTGCCTCTCAATTGAAACTCTGGCCGCTTATGCACACGAACTGGCAGAGTGGGTTCTGGGCCAGGAAAGTGTACTTGCTc                              >  1:320305/1‑139 (MQ=255)
                                                                                                    tACCGTCAAATTGCACCAGCCCGCGAAGTTGATGTGGCACGCTGCCTCTCAATTGAAACTCTGGCCGCTTATGCACACGAACTGGCAGAGTGGGTTCTGGGCCAGGAAAGTGTACTTGCTGCACTGGTTTTTGCCACCg            >  2:752574/1‑139 (MQ=255)
                                                                                                       cGTCAAATTGCACCAGCCCGCGAAGTTGATGTGGCACGCTGCCTCTCAATTGAAACTCTGGCCGCTTATGCACACGAACTGGCAGAGTGGGTTCTGGGCCAGGAAAGTGTACTTGCTCCACTGGTTTTTGCCACCGCCa         >  2:595512/1‑139 (MQ=255)
                                                                                                              ttGCACCAGCCCGCGAAGTTGATGTGGCACGCTGCCTCTCAATTGAAACTCTGGCCGCTTATGCACACGAACTGGCAGAGTGGGTTCTGGGCCAGGAAAGTGTACTTGCTCCACTGGTTTTTGCCACCGCCAGCACTGa  >  1:414242/1‑139 (MQ=255)
                                                                                                                           |                                                                                                                             
AAACGGTAACCAGGCTCGCAAAGCAGGGCGTCCGCTCGCTGGGCGCGGCGTAGTGCTCTCCGGTTCATGCTCTCAAATGACCAACCGCCAGGTAGCACATTACCGTCAAATTGCACCAGCCCGTGAAGTTGATGTGGCACGCTGCCTCTCAATTGAAACTCTGGCCGCTTATGCACACGAACTGGCAGAGTGGGTTCTGGGCCAGGAAAGTGTACTTGCTCCACTGGTTTTTGCCACCGCCAGCACTGA  >  NC_000913/2863042‑2863290

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A