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
A18 F5 I1 R1 16 23.8 843492 94.0% 792882 143.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913_3_pae_tpiA 2,817,170 C→A E112* (GAA→TAA)  yqaB ← fructose‑1‑P and 6‑phosphogluconate phosphatase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913_3_pae_tpiA2,817,1700CA94.4% 34.6 / NA 18E112* (GAA→TAA) yqaBfructose‑1‑P and 6‑phosphogluconate phosphatase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  major base A (7/10);  minor base G (1/0);  total (8/10)
Fisher's exact test for biased strand distribution p-value = 4.44e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CACGCCCATACGCTGCGCGCACAACAAAAATGTGTCTGGCGCGGGTT‑TATGGTGTTTGACGTGATCGGCAGCGACGACGGCGTCAAAATAATGGCGTAATCCCAGGTGCGCCAGCAATGCCTCAGCGATGGCGCTTTCACTCCCCGTTCCTACAGCCATTGGGCGACGACCATGCCAACTTTTCACCACATCAACAAGAGGAAGCGGTTCGACGCTATCCAGCAGCATACTTCTTACTGCTTCTGTTTTTTCACGCGCTAACGCATGCGGGTCGAGATCGGC  >  NC_000913_3_pae_tpiA/2817033‑2817314
                                                                                                                                          |                                                                                                                                                
cACGCCCATACGCTGCGCGCACAACAAAAATGTGTCTGGCGCGGGTT‑TATGGTGTTTGACGTGATCGGCAGCGACGACGGCGTCAAAATAATGGCGTAATCCCAGGTGCGCCAGCAATGCCTCAGCGATGGCGCTTTAACTCCCCGTTc                                                                                                                                       <  1:316390/149‑1 (MQ=255)
 aCGCCCATACGCTGCGCGCACAACAAAAATGTGTCTGGCTCGGGGT‑TATAGTGTCTGACGTCATCGGCAGCGACGACGGCGTCAAAATAATGGCGTAATCCCAGGTGCGCCAGCAATGCCTCCGCGATGGCGCCTTGACTCCCCGCTcc                                                                                                                                      >  2:91157/1‑149 (MQ=255)
 aCGCCCATACGCTGCGCGCACAACAAAAATGTGGCTGGCGCGGGAT‑TATGGTGTTTGACGTGATCGGCAGCGACGACGGCGTCAAAATAATGGCATAAACCCAGAGGCGCCAGCCATGCCTCAGCGCTGGCGCTTTAACTCCCCGttac                                                                                                                                      >  2:88636/1‑147 (MQ=255)
   gCCCATACGCTGCGCGCACAACAAAAATGTGTCTGGCGCGGGTT‑TATGGTGTTTGACGTGATCGGCAGCGACGACGGCGTCAAAATAATGGCGTAATCCCAGGTGCGCCAGCAATGCCTCAGCGATGGCGCTTTAACTCCCCGTTCCTa                                                                                                                                    <  2:283050/149‑1 (MQ=255)
     ccATACGCTGCGCGCACAACAAAAATGTGCCTCG‑GCAGTTTGTATGGTGTTTGACGTGATCGGCAGCAACGGCGGCGTCAAAATAATGGCGTAATCCCAGGTGCGCCAGCAATGCCGCAGCAGCAGCGCTCTAACTCCCCGTTCCTAcg                                                                                                                                  >  1:102026/1‑148 (MQ=255)
                      aacaaAAATGTGTCTGGCGCGGGTT‑TATGGTGTTTGACGTGATCGGCAGCGACGACGGCGTCAAAATAATGGCGTAATCCCAGGTGCGCCAGCAATGCCTCAGCGATGGCGCTTTAACTCCCCGTTCCTCCAGCCATTGGGCGACGAcc                                                                                                                 >  1:333073/1‑149 (MQ=255)
                      aacaaAAAGGTGTCTGGCGCGGGTT‑TATGGTGTGTGACGTGATCGGCAGCGACGACGGCGTCTAAATAATGGCGTAATCCCAGGTGCGCCAGCAATGCCTCAGCGATGGTGCTTTAACTCCCCGTTCCTACAGCCATTGGGCGACGAcc                                                                                                                 <  2:374351/149‑1 (MQ=255)
                                   cTGGCGCGGGTT‑TATGGTGTTTGACGTGATCGGCAGCGACGACGGCGTCAAAATAATGGCGTAATCCCAGGTGCGCCAGCAATGCCTCAGCGATGGCGCTTTAACTCCCCGTCCCTACAGCCATTGGGCGACGACCATGCCAACTCTTc                                                                                                    >  1:256930/1‑149 (MQ=255)
                                              t‑tATGGTGTTTGACGTGATCGGCAGCGACGACGGCGTCAAAATAATGGCGTAATCCCAGGTGCGCCAGCAATGCCTCAGCGATGGCGCTTTAACTCCCCGTTCCTACAGCCATTGGGCGACGACCATGCCAACTTTTCACCACATcaac                                                                                         <  2:220848/149‑1 (MQ=255)
                                               gtacggTGTTTGACGTGATCTGGAGCGACGACTGCGTCAAAATAATGGCCTAATCCCAGGTGCGCCAGCAATGCCTCAGCGAGGGCGCTTTATCTCCCCGTTCCTACAGCCATTGTGCGACGACCATGCCAACTTTTCACCACATcagc                                                                                         <  2:287826/145‑3 (MQ=255)
                                                   ggTGTTTGACGTGATCGGCAGCGACGACGGCGTCAAAATAATGGCGTAATCCCAGGTGCGCCAGCAATGCCTCAGCGATGGCGCTTTAACTCCCCGTTCCTACAGCCATTGGGCGACGACCATGCCAACTTTTCACCACATCAACAaga                                                                                     <  1:255333/149‑1 (MQ=255)
                                                                 ccGGCAGCGAGGACGGCGTCAAAATAATGGCGTAATCCCAGGTGCGCCAGCAATGCCCCAGCGATGGCGCTTTAACTCCCCGTTCCTACAGCCATTGGGCGACGACCATGCCAACCTTTCACCACATCAACAAGAGGAAGCGGTTCGAc                                                                       <  1:343239/148‑1 (MQ=255)
                                                                                                   aTCCCAGGTGCGACAGCAATGCCTCAGCGATGGCGCTTTAACTCCCCGTTCCTACAGCCATTGGGCGACGACCATGCCAACTTTTCACCACATCAACAAGAGGAAGCGGTTCGACGCTATCCAGCAGCATACTTCTTACTGCTTCTGtt                                     <  1:176792/149‑1 (MQ=255)
                                                                                                         ggTGCGCCAGCAATGCCTCAGCGATGGCGCTTTAACTCCCCGTTCCTACAGCCATTGGGCGACGACCATGCCAACTTTTCACCACATCAACAAGAGGAAGCGGTTCGACGCTATCCAGCAGCATACTTCTTACTGCTTCTGTTTTTTCa                               <  1:367019/149‑1 (MQ=255)
                                                                                                                cAGCAATGCCTCAGCGATGGCGCTTTAACTCCCCGTTCCTACAGCCATTGGGCGACGACCATGCCAACTTTTCACCACATCAACAAGAGGAAGCGGTTCGACGCTATCCAGCAGCATACTTCTTACTGCTTCTGTTTTTTCACCCGCTa                        >  2:229111/1‑149 (MQ=255)
                                                                                                                                     gcTTTAACTCCCCGTTCCTACAGCCATTGGGCGACGACCATGCCAACTTTTCACCACATCAACAAGAGGAAGCGGTTCGACGCTATCCAGCAGCATACTTCTTACTGCTTCTGTTTTTTCACGCGCTAACGCATGCGGGGCGAGATCgg   >  1:420397/1‑149 (MQ=255)
                                                                                                                                      cTTTAACTCCCCGTTCCTACAGACATTGGGCGACGACCATGCCAACTTTTTACCACATCAACAAGAGGAAGCGGTTCGACGCTATCCAGCAGCATACTTCTTACTGCTTCTGTTTTTTCACGCGCTAACGCATGCGGGTCGAGATCGGc  <  2:264246/149‑1 (MQ=255)
                                                                                                                                       tttAACTCCCCGTTCCTACAGCCATTGGGCGACGACCATGCCAACTTTTCACCACAt                                                                                             >  1:130881/1‑57 (MQ=255)
                                                                                                                                          |                                                                                                                                                
CACGCCCATACGCTGCGCGCACAACAAAAATGTGTCTGGCGCGGGTT‑TATGGTGTTTGACGTGATCGGCAGCGACGACGGCGTCAAAATAATGGCGTAATCCCAGGTGCGCCAGCAATGCCTCAGCGATGGCGCTTTCACTCCCCGTTCCTACAGCCATTGGGCGACGACCATGCCAACTTTTCACCACATCAACAAGAGGAAGCGGTTCGACGCTATCCAGCAGCATACTTCTTACTGCTTCTGTTTTTTCACGCGCTAACGCATGCGGGTCGAGATCGGC  >  NC_000913_3_pae_tpiA/2817033‑2817314

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A