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
A4 F100 I1 R1 20 53.2 1816442 95.1% 1727436 143.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913_3_hsa_tpiA 2,679,525 G→T A1074D (GCT→GAT)  yphG ← DUF4380 domain‑containing TPR repeat protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913_3_hsa_tpiA2,679,5250GT97.4% 107.8 / NA 41A1074D (GCT→GAT) yphGDUF4380 domain‑containing TPR repeat protein
Reads supporting (aligned to +/- strand):  ref base G (0/1);  new base T (16/22);  total (16/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.88e-01

AGGGTTTTTATTAACAACGGCTTATTCTAATTATTTTGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAAGCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCATACAGCGACAACAAGTCAGGT  >  NC_000913_3_hsa_tpiA/2679380‑2679668
                                                                                                                                                 |                                                                                                                                               
aGGGTTTTTATTAACAACGGCTTATTCTAATTATTTTGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGACAGTGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCg                                                                                                                                              <  1:713309/149‑1 (MQ=255)
                   gCTTATTCTAATTATTTTGTGATGAGGGGCAATGCGTGCAGCTCAAATATTACAGTTAATAGGGTTTAGTGAACTCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTc                                                                                                                           <  2:631262/149‑1 (MQ=255)
                    cTTATTCTAATTATTTTGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCa                                                                                                                          <  1:545286/149‑1 (MQ=255)
                       aTTCTAATTATTTTGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAgcg                                                                                                                       >  1:190936/1‑149 (MQ=255)
                              ttattTTGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAg                                                                                                                >  1:65615/1‑149 (MQ=255)
                               tactttGTGATGAGCGGCAGCGTGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGa                                                                                                               <  1:189136/146‑1 (MQ=255)
                                       gatgaGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATAtt                                                                                                       <  1:86997/149‑1 (MQ=255)
                                          gaGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGAGTAATCGCCGTCAATTCAGCGCGAGCACACTCATATTgcg                                                                                                    >  2:740878/1‑149 (MQ=255)
                                           aGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTAAGAGCAGTTAAAAATAAAAGGCATCACGGTTGTGTATTATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTgcgc                                                                                                   <  2:190936/149‑1 (MQ=255)
                                               gCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTGGGCCAATCCGGATTAATCGCCGTCAATTCAGCGATAGCAGACTCATATTTCGCAAcc                                                                                               >  2:546274/1‑149 (MQ=255)
                                                 aGCGCGTGCCGCTCAAATATTACAGTTAATAGTGTTGAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCAACGAATCAGCGCGAGCAGACTCATATTGCGCAACCTc                                                                                             <  2:649600/149‑1 (MQ=255)
                                                    gcgTGCCGCTCAAATATTACAGTTAATAGGGGTTAGAGAACGCGGATAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTGTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTcccc                                                                                          <  2:303682/149‑1 (MQ=255)
                                                      gcgCCGCTTAAATATTACAGTTAATAGGGTTTAGTACACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGa                                                                                        <  2:390826/147‑1 (MQ=255)
                                                        gCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATACAAGGCCTCACGGTGGTGAATAATGCCGCTTTCGACCAATCCGGATTAATCGCCGTCAATTCACCGCGAGCCGCCACATATACCGCAACCTCCCCGaac                                                                                      >  2:302841/1‑147 (MQ=255)
                                                           gCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTccc                                                                                   <  1:407982/149‑1 (MQ=255)
                                                              cAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCGGGATTAATCGCCGTGAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCcgcg                                                                                <  1:796427/149‑1 (MQ=255)
                                                              cAAACATTACAGTTAATAGGGTTTAGTGAACGAGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCTGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCcgcg                                                                                <  1:684593/149‑1 (MQ=255)
                                                                          ttAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATc                                                                    <  2:652367/149‑1 (MQ=255)
                                                                          ttAAGAGGGTTTAGTTATCGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGGCAATTCAGCGCGAGCAGACGCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATc                                                                    <  2:621011/149‑1 (MQ=255)
                                                                            aaTAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACCCCAGCATCGc                                                                  >  2:254471/1‑149 (MQ=255)
                                                                              tAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGcca                                                                >  1:54428/1‑149 (MQ=255)
                                                                                    ttAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCa                                                          <  1:383191/149‑1 (MQ=255)
                                                                                       gTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGc                                                       <  2:270409/149‑1 (MQ=255)
                                                                                       gTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGc                                                       >  1:298383/1‑149 (MQ=255)
                                                                                        tGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCa                                                      >  1:508728/1‑149 (MQ=255)
                                                                                        tGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCa                                                      >  1:229224/1‑149 (MQ=255)
                                                                                                      aaTAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGCGTCCCGCGGACGCCAGCATCGCCACCATCCGGCCTTTTTGTTTAtgct                                        >  1:802752/1‑149 (MQ=255)
                                                                                                        tAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTAtgctgc                                      >  1:815765/1‑149 (MQ=255)
                                                                                                         aaaaGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATgctgct                                     <  2:156167/149‑1 (MQ=255)
                                                                                                            aGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCtgtt                                  >  2:161204/1‑149 (MQ=255)
                                                                                                                      gtgcttgataatGCGGCTTTCGGCCAAACCGTATTAAGCTCCGTCCATTTATCTCGAGCAGTCGCATATTGCGCAACCGCCCCCAGTCGCGCTGACGCCAGGAGCGTCACCTTCAGGCATTTTTCGTTATGCTGCTGTTGTAAATCGcc                        <  2:26160/142‑1 (MQ=255)
                                                                                                                       tggtgAATGATGCCGCTTTCGGCAAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCGGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCa                       <  2:462809/149‑1 (MQ=255)
                                                                                                                       tggtgAATATGTCCGCTTTCGGCCAATTCGGATTAATCGCCGTCAATTCAGCGCTGGCAGACTCATATTGCGCATCCTCCCCTAGTTCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCa                       <  2:886646/149‑1 (MQ=255)
                                                                                                                            aataatGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCATACAg                  >  2:843770/1‑149 (MQ=255)
                                                                                                                                atGCCGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCATACAGCGac              <  2:65615/149‑1 (MQ=255)
                                                                                                                                   ctgttttCGGCGAGTCCGTATTAATCGCCGGCAATTCATCGCGAGCATCCTTATTTTGCGCAACCTCTCCGAGTCCCGCGGACGCCAGCATCGCCACCACCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCATACAGCGacaac           <  2:302559/145‑1 (MQ=255)
                                                                                                                                    cGCTTTCGGCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCATACAGCGacaaca          >  2:769427/1‑149 (MQ=255)
                                                                                                                                        ttgggCCAATTCGGATTAGTCGCCGTCAATTCAGCGCGAGCAGTCTCAGATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCATACAGCGACAACAAGTc      <  1:169524/146‑1 (MQ=255)
                                                                                                                                        tgcGGCCAGGCCGGATTAATCGGCGTCAATTCAGCGCGAGCAGACTCTTATTGTGCAAACTCGCCGAGTCCCGCGGACGCCAGCATCGCCACGATCTGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCATACAGCGACAACAAGTc      <  2:228452/147‑1 (MQ=255)
                                                                                                                                          cGGCCAACCCGCATTAATCGCCGTCAATTCAGCCCGAGCATACTCATCTTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCTCTACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCATACAGCGACAACAAGTCAg    <  1:144963/149‑1 (MQ=255)
                                                                                                                                            gCCAATCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCGTATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCATACAGCGACAACGAGTCAGGt  >  1:862159/1‑149 (MQ=255)
                                                                                                                                                 |                                                                                                                                               
AGGGTTTTTATTAACAACGGCTTATTCTAATTATTTTGTGATGAGCGGCAGCGCGTGCCGCTCAAATATTACAGTTAATAGGGTTTAGTGAACGCGGTTAAAAATAAAAGGCATCACGGTGGTGAATAATGCCGCTTTCGGCCAAGCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAGGCATTTTTCTTTATGCTGCTGTTGTAAATCGCCATACAGCGACAACAAGTCAGGT  >  NC_000913_3_hsa_tpiA/2679380‑2679668

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