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
A8 F9 I0 R1 23 38.9 1378630 88.6% 1221466 148.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913_3_hsa_tpiA 2,976,638 T→G 61.1% S14A (TCA→GCA)  galR → galactose‑inducible d‑galactose regulon transcriptional repressor; autorepressor

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913_3_hsa_tpiA2,976,6380TG61.1% 15.0 / 25.1 37S14A (TCA→GCA) galRgalactose‑inducible d‑galactose regulon transcriptional repressor; autorepressor
Reads supporting (aligned to +/- strand):  ref base T (8/6);  new base G (14/8);  total (23/14)
Fisher's exact test for biased strand distribution p-value = 7.38e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.22e-01

ATTTGCGTTTGGCTCACATTCCCACGATGAAAACACGCCACCCCTTGAACCAACGGGCGTTTTCCGTAACACTGAAAGAATGTAAGCGTTTACCCACTAAGGTATTTTCATGGCGACCATAAAGGATGTAGCCCGACTGGCAGGCGTTTCAGTCGCCACCGTTTCCCGCGTCATTAATAATTCACCCAAAGCCAGCGAAGCTTCCCGGCTGGCTGTGCATAGTGCAATGGAGTCTCTTAGCTATCACCCGAACGCCAACGCCCGTGCGCTGGCGCAGCAGACCACTGAAACGGTC  >  NC_000913_3_hsa_tpiA/2976490‑2976784
                                                                                                                                                    |                                                                                                                                                  
atgtGCGTTTGGCTCACATTCCCACGATGAAAACACGCCACCCCTTGAACCAACGGGCGTTTTCCGTAACACTGAAAGAATGTAAGCGTTTACCCACTAAGGTATTTTCATGGCGACCATAAAGGATGTAGCCCGACTGGCAGGCGttt                                                                                                                                                    <  2:136290/146‑1 (MQ=255)
aTTTGCGTTTGGCTCACATTCCCACGATGAAAACACGCCACCCCTTGAACCAACGGGCGTTTTCCGTAACACTGAAAGAATGTAAGCGTTTACCCACTAAGGTATTTTCATGGCGACCATAAAGGATGTAGCCCGACTGGCAGGCGttt                                                                                                                                                    <  2:211531/149‑1 (MQ=255)
     cGTTTGGCTCACATTCCCACGATGAAAACACGCCACCCCTTGAACCAACGGGCGTTTTCCGTAACACTGAAAGAATGTAAGCGTTTACCCACTAAGGTATTTTCATGGCGACCATAAAGGATGTAGCCCGACTGGCAGGCGTTTCAGTc                                                                                                                                               <  1:535335/149‑1 (MQ=255)
     cGTTTGGCTCACATTCCCACGATGAAAACACGCCACCCCTTGAACCAACGGGCGTTTTCCGTAACACTGAAAGAATGTAAGCGTTTACCCACTAAGGTATTTTCATGGCGACCATAAAGGATGTAGCCCGACTGGCAGGCGTTGCAGTc                                                                                                                                               <  2:409466/149‑1 (MQ=255)
     cGTTTGGCCCACATTCCCACGATGAAAACACGCCACCCCTTGAACCAACGGGCGTTTTCCGTAACACTGAAAGAATGGAAGCGTTTACCCACTAAGGTATTTTCATGGCGACCATAAAGGATGTAGCCCGACTGGCAGGCGTTTCAGTc                                                                                                                                               <  1:344866/149‑1 (MQ=255)
     agTTTGGCTCACATTCCCACGGTGAAAACACGCACTCCCTTGAAGCAACGGGCGTTTTACGTAACTCTGAAAGAAGTTAAGCGTTTACCCACTAAGGTATTTTCATGGCGACCATAAAGGATGTAGCCCGACTGGCAGGCGTTTCAGTc                                                                                                                                               <  2:417248/148‑1 (MQ=255)
      gTTTGGCTCACATTCCCACGATGAAAACACGCCACCCCTTGAACCAACGGGCGTTTTCCGTAACACTGAAAGAATGTAAGCGGTTACCCACAAAGGTATGTGCATGGCGACCATAAAGGATGTAGCCCGACTGGCAGGCGTTACAGtgg                                                                                                                                              >  1:121495/1‑147 (MQ=255)
             tCACATTCCCACGATGAAAACACGCCACCCCTTGAACCAACGGGCGTTTTCCGTAACACTGAAAGAATGTAAGCGTTTACCCACTAAGGTATTTTCATGGCGACCATAAAGGATGTAGCCCGACTGGCAGGCGTTGCAGTCGCCACCGt                                                                                                                                       >  1:177201/1‑149 (MQ=255)
             tCACATTCCCACGATGAAAACACGCCACCCCTTGAACCAACGGGCGTTTTCCGTAACACTGAAAGAATGTAAGCGTTTACCCACTAAGGTATTTTCATGGCGACCATAAAGGATGTAGCCCGACTGGCAGGCGTTGCAGTCGCCACCGt                                                                                                                                       >  1:177841/1‑149 (MQ=255)
              caaactCCAACGATAGAAACACGAAACTCCTTGAACGAGCGTGCTTTTTCCGTAACACGGAAAGAATGTAAGCGGTTACCCACTAAGGTATTTTCATGGCGACCATAAAGGATGTAGCCCGACTGGCAGGCGTTGCAGTCGCCCCCGtt                                                                                                                                      >  2:62942/6‑149 (MQ=255)
                  ttCCCACGATGAAAACACGCCACCCCTTGAACCAACGGGCGTTTTCCGTAACACTGAAAGACTGTAAGCGTTTACCCACTAAGGTATTTTCATGGCGACCATAAATGATGTAGCCCGACTGGCGGACGTTTCAGTGGCCACCGTTTccc                                                                                                                                  >  2:610033/1‑149 (MQ=255)
                     ccACGATGAAAACACGCCACCCCTTGAACCAACGGGCGTTTTCCGTAACACGGAAAGAATGTAAGCGTTTACCCACTAAGGTATTTTCATGGCAGCCATAAAGGATGTAGCCCGACTGACAGGCGTTGCAGTCGCAACCGTTTTCcgcg                                                                                                                               >  2:295985/1‑149 (MQ=255)
                         gATGAAAACACGCCACCCCTAGAACCAACGGGCGTTTTCCGTAACACTGAAAGAATGTAAGCGTTTACCCACTAAGGTATTGTCATGGCGACCATAAAGGATGTAGCCCGCCTGGCAGGCGTTTCACTCGCCACGGTTTCCCGCGCCAt                                                                                                                           >  2:249977/1‑149 (MQ=255)
                                  acGCCACCCCTTGAACCAACGGGCGTTTTCCGTAACACTGAAAGAATGTAAGCGTTTACCCACTAAGGTATTTTCATGGCGACCATAAAGGATGTAGCCCGACTGGCAGGCGTTTCAGTCGCCCCCGTTTCCCGCGTCATTAATAATTc                                                                                                                  >  2:265136/1‑149 (MQ=255)
                                      cACCCCTTGAACCAACGGGCGTTTTCCGTAACACTGAAAGAATGTAAGCGTTTACCCACTAAGGTATTTTCATGGCGACCATAAAGGATGTCGTCAGACTGGCAGGCGTTGCAGTCGCCACCGTTTCCCGCGTCATTAATAATTCAccc                                                                                                              >  1:472516/1‑149 (MQ=255)
                                         gccgtGAACCAGCGGGCGTTTTCTGTAACACTGAAAGAATGTAACCGTTTACCCACTAAGGTATTTTCATGGCGACCATAAAGGATGTAGCCCGACTGGCAGGCGTTTCAGTCGCCACCGTTTCCCGCGTCATTAATAATTCACCCaaa                                                                                                           <  2:34372/145‑1 (MQ=255)
                                            ttGAACCAACGGGCGTTTTCCGTAACACTGCAAGAATGTAAGCGTTTACCCACTAAGGTATTTTCATGGCGACCATAAAGGATGTAGCCCGACTGGCAGGCGTTGCAGTCGCCACCATTTCCCGCGTCATTAATAATTCACCCCAAGcc                                                                                                        >  1:163966/1‑149 (MQ=255)
                                            ttGAACCAACGGGCGTTTTCCGTAACACTGAAAGAATGTAAGCGTTTACCCACTAAGGTATTTTCATGGCGACCATAAAGGATGTAGCCCGACTGGCAGGCGTTTCAGTCGCCACCGTTTCCCACGTCATTACTAATTAACCCAAAGcc                                                                                                        >  2:521989/1‑149 (MQ=255)
                                                aCCAACGGGCGTTTTCCGTAACACTGAAAGAATGTAAGCGTTTACACACTAAGGTATTTTCATGGCGACCATAAAGGATGTAGCCCGACTGGCAGGCGTTTCCATCGCCACCGTTTCCCGCCTAATTAATAATTCAACCAAAGCCAGCg                                                                                                    >  2:299964/1‑149 (MQ=255)
                                                   aaCGGGCGTTTTCCGTAACACTGAAAGAATGTAAGCGTTTACCCACTAAGGTATTTTCATGGCGACCATAAAGGATGTAGCCCGACTGGCAGGCGTTTCAGTCGCCACCGTTTCCCGCGTCGTTAATAATTCACCCAAAGCCAGCGacg                                                                                                 >  1:7994/1‑147 (MQ=255)
                                                                      acTGAAAGAATGTAAGCGTTTACCCACTAAGGTATTTTCATGGCGACCAGAAAGGATATAGCCCGACTGGCAGGCGTTGCAGTCGCCACCGTTTCCCGCGTCATTAATAATTCCCCCAAAGCCAGCGAAACTTCCCCGCTGGCTCTGCa                                                                              >  2:532629/1‑149 (MQ=255)
                                                                        tGAAAGAATGTAAGCGTTTACCCACTAAGGTATTTTCATGACGACCATAAAGGATGTTCTCCGAGTGCCAGGCTAGGCTGTTCCCAACGTCTACCCACTCCGTAATGATTCACCCAAAGCCAGCGAAGCTTCCCGCCTGCACGTGCATa                                                                            >  2:341225/1‑149 (MQ=255)
                                                                         gAAAGAATGTAAGCGTTTACCCACTAAGGTATTGTCATGGCGACCATAAAGGATGTAGCCCGACTGGCAGGCGTTGCAGTCGCCACCGTTTCCCGCGTCATTAATAATTCACCCAAAGCCAGCGAAGCTTCCCGGCTGGCTGTGCATAg                                                                           <  2:222142/149‑1 (MQ=255)
                                                                          gaaGAATGTAAGCGTTTACCCACTCAGGTAGTTTCATGGCGACCATAAAGGATGTAGCCCGACTGGCAGGCGTTGCAGTCGCCACCGTTTCCCGCGTCATTAATAATTCACCCAAAGCTTTGGAAGCTTCCCGGTTGGCTGTGCATAGt                                                                          <  2:659125/148‑1 (MQ=255)
                                                                          aaaGAATGTAAGGCTTTACCCAATAAGGTATTTTCATGGCGACCATAAAGGATGTAGCCCGACTGGCAGGCGTTGCAGTCGCCACCGTTTCTCGCGTCATTAATAATTCACCCAAAGCCAGCGAAGCTTCCCGGCTGGCTGTGCATAGt                                                                          <  2:107496/149‑1 (MQ=255)
                                                                             gAATGTAAGAGTTTATCCACTAAGGTATTTTCATGGCGACCATAAAGGAAGTAGCACGGCTGGCAGGCGTTTCAGTCGCCACCGTTTCCCGCGTCATTTATAGTTCACCCTAGGCCAACGAAACTTCCCGGCTGGCTGTGGATGATGCa                                                                       >  2:468521/1‑149 (MQ=255)
                                                                              aaTGTAAGCGTTTACCCACTAAGGTATTTTCATGGCGACCATAAAGGATGTAGCCCGACTGGCAGGCGTTTCAGTCGCCACCGTTTCCCGCGTCATTAATAATTCACCCAAAGCCAGCGAAGCTTCCCGGCTGGCTGTGCATAGTGCaa                                                                      <  2:511904/149‑1 (MQ=255)
                                                                               aTGGAAGCGTTTACCCCATAAGGTATTTTCATGCGCACCATATAGGATGTAGCCCGACTGGCAGGCGTTGCAGTCGCCACCGTTTCCCGCGTCATTAATAATTCACCCAAAGCCAGCGAAGCTTCCCGGCTGGCTGTGCATAGTGCAAt                                                                     <  2:279041/149‑1 (MQ=255)
                                                                                  tAAGCGTTTACCCACTAAGGTATTTTCATGGCGACCATAAAGGATGTAGCCCGACTGGCAGGCGTTGCAGTCGCCACCGTTTCCCGCGTCATTAATAATTCACCCAAAGCCAGCGAAGCTTCCCGGCTGGCTGTGCATAGTGCAATGGa                                                                  <  1:683356/149‑1 (MQ=255)
                                                                                            cccAGTATGGTATCTTCATGGCGATCATAAAGGAGGTAGCACGATTGGCAGGCGTTGCAGTCGCCGCCGTTTCCCGCGTCATTAATAATTCACCCATCGCCAGCGAAGCTTCCCGGCTGGCTGTGCATAGTTCAATGGAGTCTCTTAGc                                                        <  2:48993/149‑1 (MQ=255)
                                                                                               aCTAAGGTATTTTCATGGCGACCATAAAGGATGTAGCCCGACTGGCAGGCGTTGCAGTCGCCACCGTTTCCCGCGTCATTAATAATTCACCCAAAGCCAGCGAAGCTTCCCGGCTGGCTGTGCATAATGCAAAGGAGACTCTTAGCTAt                                                     >  1:426509/1‑149 (MQ=255)
                                                                                                          ttCCTGGCGACCATAAAGGATGTAGCCCGACTGGCAGGCGTTGCAGTCGCCACCGTTTCCCGCGTCATTAATAATTCACCCAAAGCCAGCGAAGCTTCCCGGCTGGCTGTGCATAGTGCAATGGAGTCTCTTAGCTATCACCCGaacgc                                          <  1:228257/149‑1 (MQ=255)
                                                                                                             aTGGCGACCATAAAGGATGTAACCCGACTGGCAGGCGTTTCAGTCGCCACCGTTTCCCGCGTCATTAACAATTCACCCACAGCCAGCGAAGCTTCCCGCCTGGCTGTCCATAGTGCAACGGAGCCTCTTCGCTATCAACCGcacgccac                                       >  2:608225/1‑148 (MQ=255)
                                                                                                              tGGCGACCATAAAGGATGTAGCCCGACTGGCAAGCGTTGCAGTCGCCACGGTTTACCGCGTCATTAATAATTCACCCAAAGCCCGCGAAGCTTCCCGGCTGGCTGTGCATAGTGCGATGGAGCCGCATACCTATCTCCCGaacgccaca                                      >  2:212217/1‑147 (MQ=255)
                                                                                                                         aaGGATGTAGCCCGACTGGCAGGCGTTGCAGTCGCCACCGTTTCCCGCGTCATTAATAATTCCCCCAAAGCCAGCGAAGCTTCACGGGTGGCTGTGCATAGTGCAATGGAGGTTCTTACCTATCCCCCGACAGCCAACGCCCGtcggct                           >  2:217278/1‑144 (MQ=255)
                                                                                                                          aGGATGTAGCCCGACTGGCAGGCGTTGCAGTCGCCACCGTTTCCCGCGTCATTAATAATTCACCCAAAGCCCGCGAAGCTTCCCGGCTGGCTGTGCATCGTGCAATGGAGTCTCTTAGCTATCACCCGAACGCCACCCGCCGTgcgccg                          >  1:258110/1‑147 (MQ=255)
                                                                                                                                  gCCCGACTGGCAGGCGTTGCAGTCGCCACCGTTTCCCGCGTCATTAATAATTCACCCAAAGCCAGCGAAGCTTCCCGGCTGGCTGTGCATAGTGCAATGGAGTCTCTTAGCTATCACCCGAACGCCAACGCCCGTGCGCTGGCgcagca                  >  2:462584/1‑149 (MQ=255)
                                                                                                                                    ccGACTGGCAGGCGTTGCAGTCACAACCGTTTCCCGCGCCATTAATAATTCACCCAAAGCCAGCGAAGCTTCCCGGCTGGCTGTGCATAGCGCAATGGAGTCTCTTAGCTATCACCCGAACGCCAACGCCAGTACGCTGACGcagcagc                >  2:115340/1‑148 (MQ=255)
                                                                                                                                             aGGCGTTTCAGTCGCCACCGTTTCCCGCGTCATTAATAATTCACCCAAAGCCAGCGAAGCTTCCCGGCTGGCTGTGCATAGTGCAATGGAGTCTCTTAGCTATCACCCGAACGCCAACGCCCGTGCGCTGGCGCAGCAGACCACTGcaa       <  1:655280/149‑1 (MQ=255)
                                                                                                                                                 gtctCAGTCGCCACCGTTTCCCGCGTCATTAATAATTCACCCAAAGCCAGCGAAGCTTCCCGGCTGGCTGTGCATAGCGCAATATGGTCTCTTAGCTATCATCCGAACGCCACCGCCCGTGCGCTGGCGCAGCAGACCACTGAAAcggt   <  1:20226/146‑1 (MQ=255)
                                                                                                                                                  tttCAGTCGCCACCGTTTCCCGCGTCATTAATAAGTCACCCAAAGCCAGCGAAGCTCCCCGGCGGGCTGTGCATAGTGCAATGGAGTCTCTTAGCTATCACCCGAACGCCAACGCCCGTGCGCTGGCGCAGCAGACCACTGAAAcggtc  <  1:612731/149‑1 (MQ=255)
                                                                                                                                                    |                                                                                                                                                  
ATTTGCGTTTGGCTCACATTCCCACGATGAAAACACGCCACCCCTTGAACCAACGGGCGTTTTCCGTAACACTGAAAGAATGTAAGCGTTTACCCACTAAGGTATTTTCATGGCGACCATAAAGGATGTAGCCCGACTGGCAGGCGTTTCAGTCGCCACCGTTTCCCGCGTCATTAATAATTCACCCAAAGCCAGCGAAGCTTCCCGGCTGGCTGTGCATAGTGCAATGGAGTCTCTTAGCTATCACCCGAACGCCAACGCCCGTGCGCTGGCGCAGCAGACCACTGAAACGGTC  >  NC_000913_3_hsa_tpiA/2976490‑2976784

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A