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
A11 F44 I0 R1 115 55.9 2109214 91.7% 1934149 142.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 1,196,245 T→C 35.4% L375L (TTA→CTA) ‡ icd → isocitrate dehydrogenase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,196,2450TC35.4% 23.1 / 18.6 27L375L (TTA→CTA) ‡icdisocitrate dehydrogenase
Reads supporting (aligned to +/- strand):  ref base T (9/8);  new base C (3/6);  total (13/14)
Fisher's exact test for biased strand distribution p-value = 4.29e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.07e-01

TGACGAATGCGCCCTGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAG  >  NC_000913/1196109‑1196381
                                                                                                                                        |                                                                                                                                        
tGACGAATGCGCCCTGTTTGCCGCCACCCACGAAACCGTGCTTAACAGGGCCTGGCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGACGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTg                                                                                                                                    <  1:1038908/143‑1 (MQ=255)
  aCGAATGCGCCCTGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGtt                                                                                                                                  <  2:426705/143‑1 (MQ=38)
               gTTTGAAGCCACCCGCGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTATATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGTTGACCTGATTGTTAAAGGTATGGAAg                                                                                                                     <  2:1003384/143‑1 (MQ=25)
                 ttGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCCCTCCGCTGAGAGGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGgc                                                                                                                   <  1:748891/143‑1 (MQ=25)
                    aaGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAGTTGTTAAAGGTATGGAGGGCGCa                                                                                                                >  1:423285/1‑143 (MQ=255)
                         acccacGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGACATGATGCTGCGGCACATGGGTTGGACCGAAGCGGCGGGATTAATTATTGAAGGTCGTGAAGGCGCAATCac                                                                                                           >  2:738424/1‑142 (MQ=255)
                         aaccacGGTACTGCGCGTGCATATGTCGTTCAGGACAGAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATTGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCaa                                                                                                           <  2:960797/141‑1 (MQ=18)
                           ccacGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATCTGGGTTGGACTGAAGCGGCTTACCTGATCTTTATCGTTATGTAAGGCGTATTCaatg                                                                                                         >  1:290778/1‑141 (MQ=25)
                           ccacGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTGATTGTTAAAGGTATGGAAGGCGCAATCAAcg                                                                                                         >  1:793774/1‑143 (MQ=255)
                            cacGGTACTGCGCCGAAATACGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCTATACGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAAtgc                                                                                                        <  1:604930/143‑1 (MQ=21)
                               ggTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAGATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCaa                                                                                                     <  2:932884/143‑1 (MQ=21)
                               ggTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAAtgccaa                                                                                                     >  1:730939/1‑140 (MQ=21)
                               ggTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCAGAGATGATGCTGCGCCACATGGGTTGGACCGAAGAGACTGACATAATTGTTAAAGGTATGGAAGGCGCAATCAACACGaa                                                                                                     >  2:446857/1‑143 (MQ=38)
                                 tACTGCGCCGAAATATGCCCGGCAGGACAAAGTACATCCTGGCCCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGaaaa                                                                                                   <  1:390242/143‑1 (MQ=255)
                                   cTGCGCGTAAATATGCCGGTCAGGACAAAGTAAATCCCGCCTCTATTCTTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAAcc                                                                                                 <  2:733438/143‑1 (MQ=37)
                                        ccGAAATATGCCGGTCAGGACAAAGTAAATCGTGGCTCGATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAAc                                                                                            <  2:654531/143‑1 (MQ=255)
                                        ccGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAAc                                                                                            >  2:947620/1‑143 (MQ=255)
                                          gAAATATGCCGGTCAGTACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCt                                                                                          <  1:816800/143‑1 (MQ=255)
                                                  ccGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTc                                                                                  >  1:4471/1‑143 (MQ=17)
                                                                       cTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCt                                                             >  1:989879/1‑143 (MQ=255)
                                                                          gCTCGATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTaaa                                                          <  2:825754/143‑1 (MQ=255)
                                                                                                           gcCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGatc                         >  1:663129/1‑143 (MQ=255)
                                                                                                                 tGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGaa                   <  1:569386/143‑1 (MQ=255)
                                                                                                                 tGGGTTGGACCGAAGCGGCTGACTTAACTGTTACAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGaa                   <  2:532437/143‑1 (MQ=255)
                                                                                                                          ccGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTag          >  2:793280/1‑142 (MQ=255)
                                                                                                                          ccGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTaa          >  2:756407/1‑143 (MQ=255)
                                                                                                                                  gCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAg  >  1:936391/1‑143 (MQ=255)
                                                                                                                                        |                                                                                                                                        
TGACGAATGCGCCCTGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAATGCCGTAG  >  NC_000913/1196109‑1196381

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A