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 F1 I2 R1 772 77.0 3769570 91.6% 3452926 105.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,742,599 Δ1 bp intergenic (‑67/‑134) yiaJ ← / → yiaK transcriptional repressor for the yiaKLMNO‑lyxK‑sgbHUE operon/2,3‑diketo‑L‑gulonate reductase, NADH‑dependent

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,742,5980C.93.3% 49.3 / ‑2.0 15intergenic (‑66/‑135)yiaJ/yiaKtranscriptional repressor for the yiaKLMNO‑lyxK‑sgbHUE operon/2,3‑diketo‑L‑gulonate reductase, NADH‑dependent
Reads supporting (aligned to +/- strand):  ref base C (1/0);  new base . (6/8);  total (7/8)
Fisher's exact test for biased strand distribution p-value = 4.67e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.91e-01

GGCTTCCGGCTGGACGCTCTTTTTCCTGCGCCATCTCGTTCTCTTTTTTTCCCATCACTTCTTTCCCCATTTTGTCGCGTCCTGATGGTAGCGCAAAGTGTGCCGTAGTTCACGATCTCGACAGATAATTTATAACCAATTGATTTTTATGTCTTTTGAAATTCATCAATCAGATTGCC  >  NC_000913/3742463‑3742641
                                                                                                                                       |                                           
ggCTTCCGGCTGGACGCTCTTTTTCCTGCGCCATCTCGTTCTCTTTTTTTCCCATCACTTCTTTCCCCATTTTGTCGCGTCCTGATGGTAGCGCAAAGTGTGCCGTAGTTCACGATCTCGACAGATAATTTATAAcaat                                          <  1:785633/139‑4 (MQ=255)
   ttCCGGCTGGACGCTCTTTTTCCTGCGCCATCTCGTTCTCTTTTTTTCCCATCACTTCTTTCCCCATTTTGTCGCGTCCTGATGGTAGCGCAAAGTGTGCCGTAGTTCACGATCTCGACAGATAATTTATAA‑CAATTGa                                      <  1:1213027/139‑1 (MQ=255)
          tGGACGCTCTTTTTCCTGCGCCATCTCGTTCTCTTTTTTTCCCATCACTTCTTTCCCCATTTTGTCGCGTCCTGATGGTAGCGCAAAGTGTGCCGTAGTTCACGATCTCGACAGATAATTTTTAA‑CAATTGATTTTTAt                               <  1:225043/139‑1 (MQ=255)
          tGGACGCTCTTTTTCCTGCGCCATCTCGTTCTCTTTTTTTCCCATCACTTCTTTCCCCATTTTGTCGCGTCCTGATGGTAGCGCAAAGTGTGCCGTAGTTCACGATCTCGACAGATAATTTATAA‑CAATTGATTTTTAt                               <  1:1615436/139‑1 (MQ=255)
           ggACGCTCTTTTTCCTGCGCCATCTCGTTCTCTTTTTTTCCCATCACTTCTTTCCCCATTTTGTCGCGTCCTGATGGTAGCGCAAAGTGTGCCGTAGTTCACGATCTCGACAGATAATTTATAAcaat                                          <  1:125156/128‑4 (MQ=255)
           ggACGCTCTTTTTCCTGCGCCATCTCGTTCTCTTTTTTTCCCATCACTTCTTTCCCCATTTTGTCGCGTCCTGATGGTAGCGCAAAGTGTGCCGTAGTTCACGATCTCGACAGATAATTTATAAcaat                                          >  2:125156/1‑125 (MQ=255)
           ggACGCTCTTTTTCCTGCGCCATCTCGTTCTCTTTTTTTCCCATCACTTCTTTCCCCATTTTGTCGCGTCCTGATGGTAGCGCAAAGTGTGCCGTAGTTCACGATCTCGACAGATAATTTATAA‑CAATTGATTTTTATg                              >  1:1504186/1‑139 (MQ=255)
                            cgcCATCTCGTTCTCTTTTTTTCCCATCACTTCTTTCCCCATTTTGTCGCGTCCTGATGGTAGCGCAAAGTGTGCCGTAGTTCACGATCTCGACAGATAATTTATAA‑CAATTGATTTTTATGTCTTTTGAAATtcatca             <  1:698714/139‑1 (MQ=255)
                             gcCATCTCGTTCTCTTTTTTTCCCATCACTTCTTTCCCCATTTTGTCGCGTCCTGATGGTAGCGCAAAGTGTGCCGTAGTTCACGATCTCGACAGATAATTTATAActatctgtc                                     <  1:1557104/115‑9 (MQ=255)
                             gcCATCTCGTTCTCTTTTTTTCCCATCACTTCTTTCCCCATTTTGTCGCGTCCTGATGGTAGCGCAAAGTGTGCCGTAGTTCACGATCTCGACAGATAATTTATAACTATTTgtc                                     >  2:1557104/1‑113 (MQ=255)
                             gcCATCTCGTTCTCTTTTTTTCCCATCACTTCTTTCCCCATTTTGTCGCGTCCTGATGGTAGCGCAAAGTGTGCCGTAGTTCACGATCTCGACAGATAATTTATAA‑CAATTGATTTTTATGTCTTTTGAAATTCatcaa            >  2:436355/1‑139 (MQ=255)
                               cATCTCGTTCTCTTTTTCTCCCATCACTTCTTTCCCCATTTTGTCGCGTCCTGATGGTAGCGCAAAGTGTGCCGTAGTTCACGATCTCGACAGATAATTTATAA‑CAATTGATTTTTATGTCTTTTGAAATTCatcaatc          <  2:1198779/139‑1 (MQ=255)
                                 tctcGTTCTCTTTTTTTCCCATCACTTCTTTCCCCATTTTGTCGCGTCCTGATGGTAGCGCAAAGTGTGCCGTAGTTCACGATCTCGACAGATAATTTATAA‑CAATTGATTTTTATGTCTTTTGAAATTCatcaatcct        >  2:892026/1‑137 (MQ=255)
                                                         cttcttTCCCCATTTTGTCGCGTCCTGATGGTAGCGCAAAGTGTGCCGTAGTTCACGATCTCGACAGATAATTTATAA‑CAATTGATTTTTATGTCTTTTGAAATTCatcaatcctgttgac  >  1:375575/1‑113 (MQ=255)
                                                         cttcttTCCCCATTTTGTCGCGTCCTGATGGTAGCGCAAAGTGTGCCGTAGTTCACGATCTCGACAGATAATTTATAA‑CAATTGATTTTTATGTCTTTTGAAATTCatcaatcctgttgac  <  2:375575/121‑9 (MQ=255)
                                                                               tCCTGATGGTAGCGCAAAGTGTGCCGTAGTTCACGATCTCGACAGATAATTTATAA‑CAATTGATTTTTATGTCTTTTGAAATTCatcaatcctgtt     <  1:1460490/96‑6 (MQ=255)
                                                                               tCCTGATGGTAGCGCAAAGTGTGCCGTAGTTCACGATCTCGACAGATAATTTATAA‑CAATTGATTTTTATGTCTTTTGAAATTCatcaatcctgtt     >  2:1460490/1‑91 (MQ=255)
                                                                               tCCTGATGGTAGCGCAAAGTGTGCCGTAGTTCACGATCTCGACAGATAATTTATAA‑CAATTGATTTTTATGTCTTTTGAAATTCatcaat           >  1:602956/1‑90 (MQ=255)
                                                                               tCCTGATGGTAGCGCAAAGTGTGCCGTAGTTCACGATCTCGACAGATAATTTATAA‑CAATTGATTTTTATGTCTTTTGAAATTCatcaat           <  2:602956/90‑1 (MQ=255)
                                                                                                                                       |                                           
GGCTTCCGGCTGGACGCTCTTTTTCCTGCGCCATCTCGTTCTCTTTTTTTCCCATCACTTCTTTCCCCATTTTGTCGCGTCCTGATGGTAGCGCAAAGTGTGCCGTAGTTCACGATCTCGACAGATAATTTATAACCAATTGATTTTTATGTCTTTTGAAATTCATCAATCAGATTGCC  >  NC_000913/3742463‑3742641

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A