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
A7 F1 I2 R1 766 64.2 3232166 90.9% 2938038 104.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,571,902 G→A D48D (GAC→GAT)  gadB ← glutamate decarboxylase B, PLP‑dependent

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,571,9020GA87.5% 40.5 / 0.3 16coding (144/1401 nt)gadBglutamate decarboxylase B, PLP‑dependent
Reads supporting (aligned to +/- strand):  ref base G (0/0);  major base A (7/7);  minor base . (1/1);  total (8/8)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.31e-01

ATTCTTCTTTGTCGATCCAGTTTTTGTTAATGGATAAATCCATCAATTTGTGGACATTTTCGTCGTCCCAGGTCTGGCAGAAAGTGGCCAGGTTCTGACGAGCGTTGCCATCAAGATATAATTCGTCATTGATAATCTGGAATGCGACATCGTCGCGCATTTCGTGCAGCGGAAAACGTTTTGATTCTGCGATAGTGGAAATAGACTTCGCACCAAAACGTGAATCGAGTAGTTCCGACCTTAAATCCGTTACT  >  NC_000913/1571778‑1572031
                                                                                                                            |                                                                                                                                 
atTCTTCTTTGTCGATCCAGTTTTTGTTAATGGATAAATCCATCAATTTGTGGACATTTTCGTCGTCCCAGGTCTGGCAGAAAGTGGCCAGGTTCTGACGAGCGTTGCCATCAAGATATAATTCATCATTGATAATCTg                                                                                                                     <  1:1606273/139‑1 (MQ=255)
              aTCCAGTTTTTGTTAATGGATAAATCCATCAATTTGTGGACATTTTCGTCGTCCCAGGTCTGGCAGAAAGTGGCCAGGTTCTGACGAGCGTTGCCATCAAGATATAATTCATCATTg                                                                                                                             <  1:1429161/117‑1 (MQ=255)
              aTCCAGTTTTTGTTAATGGATAAATCCATCAATTTGTGGACATTTTCGTCGTCCCAGGTCTGGCAGAAAGTGGCCAGGTTCTGACGAGCGTTGCCATCAAGATATAATTCATCATTg                                                                                                                             >  2:1429161/1‑117 (MQ=255)
                                    aaTCCATCAATTTGTGGACATTTTCGTCGTCCCAGGTCTGGCAGAAAGTGGCCAGGTTCTTACGAGCGTTGCCATCAAGATATAATTCATCATTGATAATCTGAAATGCGACATCGTCGCGCATTTCGTTCAGCGGaaa                                                                                 >  1:697886/1‑139 (MQ=255)
                                          tCAATTTGTGGACATTTTCGTCGTCCCAGGTCTGGCAGAAAGTGGCCAGGTTCTGACGAGCGTTGCCATCAAGATATAATTCATCATTGATAATCTGAAATGCGACATCGTCGCGCATTTCGTGCAGCGGAAAACGttt                                                                           >  1:39791/1‑139 (MQ=255)
                                                tgtgGACATTTTCGTCGTCCCAGGTCTGGCAGAAAGTGGCCAGGTTCTGACGAGCGTTGCCATCAAGATATAATTC‑TCATTGATAATCTGAAATGCGACATCGTCGCGCATTTCGTGCAGCGGAAAACGtt                                                                            >  1:1608339/1‑131 (MQ=255)
                                                tgtgGACATTTTCGTCGTCCCAGGTCTGGCAGAAAGTGGCCAGGTTCTGACGAGCGTTGCCATCAAGATATAATTC‑TCATTGATAATCTGAAATGCGACATCGTCGCGCATTTCGTGCAGCGGAAAACGtt                                                                            <  2:1608339/131‑1 (MQ=255)
                                                  tgGACATTTTCGTCGTCCCAGGTCTGGCAGAAAGTGGCCAGGTTCTGACGAGCGTTGCCATCAAGATATAATTCATCATTGATAATCTGAAATGCGACATCGTCGCGCATTTCGTGCAGCGGAAAACGTTTTGATTCTg                                                                   <  2:39791/139‑1 (MQ=255)
                                                        ttttCGTCGTCCCAGGTCTGGCAGAAAGTGGCCAGGTTCTGACGAGCGTTGCCATCAAGATATAATTCATCATTGATAATCTGAAATGCGACATCGTCGCGCATTTCGTGCAGCGGAAAACGTTTTGATTCTGCGATAg                                                             <  2:515277/139‑1 (MQ=16)
                                                                           ggCAGAAAGTGGCCAGGTTCTGACGAGCGTTGCCATCAAGATATAATTCATCATTGATAATCTGAAATGCGACATCGTCGCGCATTTCGTGCAGCGGAAAACGTTTTGATTCTGCGATAGTGGAAATAGACTTCGCAcc                                          >  2:1176250/1‑139 (MQ=255)
                                                                            gCAGAAAGTGGCCAGGTTCTGACGAGCGTTGCCATCAAGATATAATTCATCATTGATAATCTGAAATGCGACATCGTCGCGCATTTCGTGCAGCGGAAAACGTTTTGATTCTGCGATAGTGGAAATAGACTTCGCACCa                                         >  1:778162/1‑139 (MQ=255)
                                                                                                           ccATCAAGATATAATTCATCATTGATAATCTGAAATGCGACATCGTCGCGCATTTCGTGCAGCGGAAAACGTTTTGATTCTGCGATAGTGGAAATAGACTTCGCACCAAAACGTGAATCGAGTAGTTCCGACCTTAAAt          >  2:1329927/1‑139 (MQ=255)
                                                                                                           ccATCAAGATATAATTCATCATTGATAATCTGAAATGCGACATCGTCGCGCATTTCGTGCAGCGGAAAACGTTTTGATTCTGCGATAGTGGAAATAGACTTCGCACCAAAACGTGAATCGAGTAGTTCCGACCTTAAAt          >  2:865452/1‑139 (MQ=255)
                                                                                                              tCAAGATATAATTCATCATTGATAATCTGAAATGCGACATCGTCGCGCATTTCGTGCAGCGGAAAACGTTTTGATTCTGCGATAGTGGAAATAGACTTCGCACCAAAACGTGAATCGAGTAGTTCCGACCTTAAATCCg       <  1:1329927/139‑1 (MQ=255)
                                                                                                              tCAAGATATAATTCATCATTGATAATCTGAAATGCGACATCGTCGCGCATTTCGTGCAGCGGAAAACGTTTTGATTCTGCGATAGTGGAAATAGACTTCGCACCAAAACGTGAATCGAGTAGTTCCGACCTTAAATCCg       <  1:865452/139‑1 (MQ=255)
                                                                                                                   atatAATTCATCATTGATAATCTGAAATGCGACATCGTCGCGCATTTCGTGCAGCGGAAAACGTTTTGATTCTGCGATAGTGGAAATAGACTTCGCACCAAAACGTGAATCGAGTAGTTCCGACCTTAAATCCGTTACt  <  1:1176250/139‑1 (MQ=255)
                                                                                                                            |                                                                                                                                 
ATTCTTCTTTGTCGATCCAGTTTTTGTTAATGGATAAATCCATCAATTTGTGGACATTTTCGTCGTCCCAGGTCTGGCAGAAAGTGGCCAGGTTCTGACGAGCGTTGCCATCAAGATATAATTCGTCATTGATAATCTGGAATGCGACATCGTCGCGCATTTCGTGCAGCGGAAAACGTTTTGATTCTGCGATAGTGGAAATAGACTTCGCACCAAAACGTGAATCGAGTAGTTCCGACCTTAAATCCGTTACT  >  NC_000913/1571778‑1572031

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A