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
A12 F13 I0 R1 24 46.9 828184 99.3% 822386 269.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 4,296,190 A→C 50.2% intergenic (+397/+247) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,296,1900AC50.2% ‑0.3 / 14.4 16intergenic (+397/+247)gltP/yjcOglutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
Reads supporting (aligned to +/- strand):  ref base A (5/3);  new base C (4/4);  total (9/7)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.82e-01

TATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACC  >  NC_000913/4295926‑4296471
                                                                                                                                                                                                                                                                        |                                                                                                                                                                                                                                                                                         
tATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAAACAGCGCAATAGCCTTCTTTAGCGTGATTTTGTCGGTCGGATACGGCGTTTCTGACGCATCCGACATCAACGCCTGATGCGGCGCTTAACGTGTCTTATCAGGcttcttccac                                                                                                                                                                                                                                                                   >  2:101774/1‑280 (MQ=11)
        aTCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTAGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCGGATGCAACGCTTAACGCGTCTTATCAGGCCTACGACAGCCAgcgaa                                                                                                                                                                                                                                                           >  1:200102/1‑287 (MQ=255)
                        ggcggCGACGCTTCTCGGGGTTTATCAGGCTGACGCAAGACGTCGCAATAGCCTGATTTAGCGGGATTTTGTGGGTCGGATAAGGCGTTTACGCCGCATCGGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCCGACAGGGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCATTAGCCTGATTTAGCg                                                                                                                                                                                                                                           <  2:370502/285‑1 (MQ=11)
                         gacggtaCGCTGACCGCGTCTTATGAGCGCTACGCGAGACAGAGCAATAGCCGGAGTGAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGGCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGGCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGt                                                                                                                                                                                                                                          <  2:394717/283‑1 (MQ=11)
                          aTGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATATCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCCTCCGACCTCACCGCCTGATGCGACGCTTCACGCGTCTTCTCAGGCCTACGCCCGACCGCGCAATATCCTGCATTCGCGtt                                                                                                                                                                                                                                         >  2:226044/1‑288 (MQ=11)
                                                                    gcAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACCCCGCATCCGACATCCACGCCTGATGCGACGCTTTCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTCCGCCAGCCAGCGCAATAGCCTGCTCTAGCGTGATTTTGTAGGCTGGATCAGGCGTTTACGCCGCATCCGACAt                                                                                                                                                                                                >  1:355751/1‑288 (MQ=11)
                                                                                                                      cgcATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACg                                                                                                                                                                                                                                                                       >  1:101212/1‑167 (MQ=33)
                                                                                                                      cgcATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACg                                                                                                                                                                                                                                                                       <  2:101212/167‑1 (MQ=33)
                                                                                                                                                                                                                     agtgtacggCGTTTAAGCCGCATCCGCCCGCAACGCCTGATGCGAGGCTTGCCGCGTCTTTTCAGGCCTACGCCTGCAAGCGCAATGGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTAt                                               <  2:351094/281‑1 (MQ=11)
                                                                                                                                                                                                                         tagggCGTTTAGTCCGCATCAGACATAAACGCCTGATGCGACGCTGGCCGCTGCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGGCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGc                                          <  2:186922/286‑1 (MQ=11)
                                                                                                                                                                                                                                  tacgCCGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTa                                  >  1:38180/4‑288 (MQ=17)
                                                                                                                                                                                                                                  tacgCCGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCCTATCAGGCCTATCTTa                                  >  2:381609/4‑288 (MQ=17)
                                                                                                                                                                                                                                        gCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTg                           >  2:29326/1‑289 (MQ=37)
                                                                                                                                                                                                                                                                gACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTcaca    >  2:281169/1‑288 (MQ=255)
                                                                                                                                                                                                                                                                  cGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACAcc  <  1:281169/288‑1 (MQ=255)
                                                                                                                                                                                                                                                                  cGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACAcc  <  1:29326/288‑1 (MQ=255)
                                                                                                                                                                                                                                                                        |                                                                                                                                                                                                                                                                                         
TATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACC  >  NC_000913/4295926‑4296471

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 9 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A