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
A13 F32 I0 R1 15 16.5 534746 98.2% 525120 146.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP009273 2,718,735 G→T 54.2% P124Q (CCG→CAG)  kgtP ← alpha‑ketoglutarate transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0092732,718,7350GT54.2% 4.4 / 10.1 17P124Q (CCG→CAG) kgtPalpha‑ketoglutarate transporter
Reads supporting (aligned to +/- strand):  ref base G (6/2);  new base T (5/4);  total (11/6)
Fisher's exact test for biased strand distribution p-value = 6.20e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGTCACATACTGAAATGATGCGTAAAAACCTTTGCGCCCTTCAACGGCAACTTCACTCATATAGGTGGCGCTGGTGCCATATTCTCCGCCAACAGATAATCCCTGAAATAAACGAGCGAGAAGCAATAATGCCGGAGCCCACGTACCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAACACATCATACACACCGATAACAGCATCGATTTTTTGCGACCATGTTTATCGGCTATGCGGCCAAATAGCCAACCGCCTATTGGG  >  CP009273/2718602‑2718878
                                                                                                                                     |                                                                                                                                               
cGTCACATACTGAAATGATGCGTAAAAACCTTTGCGCCCCTCAACGGCAACTTCACCCATATAGGTGGCGCTGGTGCCATATTCCTCGCCAACAGATAATCCCTGCAATAAACGAGCGAGAAGCAATAATGCCTGAGCCCACGt                                                                                                                                       <  1:102319/144‑1 (MQ=255)
         cTGAAATGATGCGTAAAAACCTTTGCGCCCTTCAACGGCAACTTCACTCATATAGGTAGCGCTGGTGCCATATTCTCCGCCAACAGATAATCCCTGAAATAAACGAGCGAGAAGCAATAATGCCTGAGCCCACGTACCTATAGTTTCAt                                                                                                                         >  2:246746/1‑149 (MQ=255)
                   gCGTAAAAACCTTTGCGCCCTTCAACGGCAACTTCACTCATATAGGTGGCGCTGGTTCCATATTCTCCGCCAACAGATAATCCCTGAAATAAACGAGCGAGAAGCAATAATGCCGGAGCCCACGTACATATAGTTTCATAACCt                                                                                                                    >  1:151862/1‑144 (MQ=255)
                    catAAAAACCTTTCCCCCCTTCAACGGCAACTTCACTCATATAGTTGGCGCTGGTGCCATATTCTCCGCCAACATATAATCCCTGAAATAAACGAGCTAGAAGCAATAATGCCTGAGCCCACGTACCTATAGTTTCATAACCTg                                                                                                                   <  1:115395/142‑1 (MQ=255)
                     gTAAAAACCTTTGCGCCCTTCAACGGCAACTTCACTCATATAGGTGGCGCTGGTGCCGTAGTCTCCGCCAACAGATAATCCCTGAAATAAACGAGCGAGAAGCAATAATGCCGGAGCCCACGTACCTATAGTTTCATAACCTGGGaggc                                                                                                             >  2:48254/1‑149 (MQ=255)
                               ttGCGCCCTTCAACGGCAACTTCACTCATATAGGTGACGCTGGTGCCATATTCTCCGCCAACAGATAATCCCTGAAATAAACGAGCGAGAAGCAATAATGCCTGAGCCCACGTACCTATAGTTTCATAACCTGGGAGGCCGGCGATAAc                                                                                                   >  2:44096/1‑149 (MQ=255)
                                      cTTCAACGGCAACTTCACTCATATAGGCGGCGCTGCTGCCATATCCTCCGCCAACAGATAATCCCTGAAATAAACGAGCGAGAAGCAATAATGCCGGAGCCCACGTACCTATAGTTTCCTAACCTGGGAGGCAGGCGATAACCa                                                                                                 <  1:94598/144‑1 (MQ=255)
                                                 aCTTCACTCATATAGGTGGCGCTGGTGCCATATTCTCCGCCAACAGATAATCCCTGAAATAAACGAGCGAGAAGCAATAATGCCGGAGCCCACGTACCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGCTCCGaaa                                                                                      >  1:64466/1‑144 (MQ=255)
                                                               ggTGGCGCTGGTGCCATATTCTCCGCCAACAGATAATCCCTGAAATAAACGAGCGAGAAGCAATAATGCCGGAGCACACGTAACTATAGTTTCATAACCTGGGAGGCCGGCGATAACCAGCGACCCGAAAAACATCATacacac                                                                        >  1:61308/1‑144 (MQ=255)
                                                                   gaccgggTGCCATATTCTCCGCCAACAGATAATCCCGGAAATAACCGAGCGAGAAGCAATAATGCCTGAGCCCACGTACCCATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAACACATCATACACACCGAt                                                                    <  1:216303/139‑1 (MQ=255)
                                                                        ggTGCCATATTCTCCGCCAACAGATAATCCCTGAAATAAACGAGCGAGAAGCAATAATGCCGGAGCCCACGTACCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGCAACACATCATACACACCGCTACCAg                                                               >  1:212844/1‑144 (MQ=255)
                                                                        cgTGCCATATTCTCGGCCAACAGATAATCCCTGAAATAAACGAGCGAGAAGCAATAATGCCTGAGCCCACGTACCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGGTCCGAAACACATCATACACACCGATAACAg                                                               >  1:143793/2‑144 (MQ=255)
                                                                                              gATAATCCCTGAAATAAACGAGCGCGCAGCAATAATGCCGGAGCCCACATACCTATAGATTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAACACATCATACACACCGATAACAGCATCGATTTTTTGCGACCATGTTTATc                                    >  2:54404/1‑149 (MQ=255)
                                                                                                          aaTCAACGAGCGAGAAGCAATAATGCCTGAGACCACGTACCTATAGTTTCATAACCTGGGAGGCAGGAGATAACAAGCGATCCGAAACACATCATACACCCCGCTACCAGCACAGGTTTTTTGCGACGAGCTTTAACGGCTCTg                             >  1:61938/1‑144 (MQ=255)
                                                                                                                               aatGCCGGAGCCCACGTACCNANAGTNTCATACCCTGGGAGGCAGGCGATAACCAGCGATCCGAAACACATCATACACACCGATAACAGCATCGATTTTTTGCGATTATGTTTATCGGTTATGCGGCTAAATAGCCAACCGCCTATTgg   <  2:134592/149‑1 (MQ=255)
                                                                                                                                atGCCTGGGCCCACGTACCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAACACTTCATAAACATCGATAAATGCATTGATTTTTTGTGTCTTTGTTTTTCGGCTATGCGGCCAAATAGCCAACCGCCTATTggg  <  2:52857/149‑1 (MQ=255)
                                                                                                                                atGCCTGAGCCCACGTACCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAACACATCATACACACCGATAACAGCATCGATTTTTTGCGACCATGTTTATCGGCTATCCGGCCAAATAGCCAACCGCCTATTggg  >  2:82572/1‑149 (MQ=255)
                                                                                                                                     |                                                                                                                                               
CGTCACATACTGAAATGATGCGTAAAAACCTTTGCGCCCTTCAACGGCAACTTCACTCATATAGGTGGCGCTGGTGCCATATTCTCCGCCAACAGATAATCCCTGAAATAAACGAGCGAGAAGCAATAATGCCGGAGCCCACGTACCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAACACATCATACACACCGATAACAGCATCGATTTTTTGCGACCATGTTTATCGGCTATGCGGCCAAATAGCCAACCGCCTATTGGG  >  CP009273/2718602‑2718878

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