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 2,796,564 G→A 19.1% V620I (GTT→ATT)  nrdE → ribonucleoside‑diphosphate reductase 2, alpha subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0092732,796,5640GA19.1% 33.1 / 3.8 21V620I (GTT→ATT) nrdEribonucleoside‑diphosphate reductase 2, alpha subunit
Reads supporting (aligned to +/- strand):  ref base G (9/8);  new base A (2/2);  total (11/10)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.03e-01

CGGCATATACAACCAGAATCTTCAGGCGGTGCCGCCAACCGGTTCTATCTCTTATATCAACCATGCTACGTCGAGTATTCATCCGATTGTGGCGAAAGTAGAGATACGCAAAGAGGGCAAAACAGGACGCGTTTACTACCCTGCCCCGTTTATGACTAACGAGAATCTGGCGCTGTATCAGGACGCTTACGAAATTGGCGCAGAAAAGATCATCGACACCTACGCGGAAGCGACTCGCCATGTCGATCAGGGGCTGTCGCTGACGCTTTT  >  CP009273/2796434‑2796703
                                                                                                                                  |                                                                                                                                           
cagCATATACAACCAGAATCTTCAGGCGGTGCCGCCAACCGGTTCTATCTCTTATATCAACCATGCTACGTCGAGTATTCATCCGATTGTGGCGAAAGTAGAGATACGCAAAGAGGGCAAAACAGGACGCGTTTACTACCCTGc                                                                                                                                >  1:179201/3‑144 (MQ=255)
       taCAACCAGAATCTTCAGGCGGTGCCCCAATGTGAACCCAACCCTTATATCAACCATGCTACGTCGAGTATTCATCCGATTGTGGCGAAAGTAGAGATACGCAAAGAGGGCCAAACAGGCCGCGTTTACTACCCTGCCCCGTTTATGAc                                                                                                                    >  2:61362/1‑149 (MQ=255)
         cAACCAGAATCTTCAGGCGGTGCCGCCAACCGGTTCTATCTCTTATATCAACCATGCTACGTCGAGTCTTCATCCGATTGTGGCGAAAGTAGAGATACGCAAAGAGGGCAAAACAGGACGCGTTTACTACCCTGCCCCGTTTAt                                                                                                                       >  1:227035/1‑144 (MQ=255)
            gcAGAATCTTCAGGCGGTGCCGCCAACCGGTTCTATCTCTTATATCAACCATGCTACGTCGAGTATTCATCCGATTGTGGCGAAAGTAGAGATACGCAAAGATGGTAAAACAGGACGCGTTTACTACCCTGCCCCGTTTATGACTAACg                                                                                                               <  2:11869/148‑1 (MQ=255)
                  tCTTCAGGCGGTGCCGCCAACCGGTTCTATCTCTTATATCAACCATACTACGTCGAGTATTCATCCAATTGTGGCGAAAGTAGAGATACGCAAAGAGGGCAAAACAGGACGCGTTTACTACCCTGCCCCGTTTATGACTAACGAGAATc                                                                                                         >  2:246173/1‑149 (MQ=255)
                                cgccAACCGGTTCTATCTCTTATATCAACCATGCTACGTCGAGTATTCATCCGATTGTGGCGAAAGTAGAGATACGCAAAGAGGGCAAAACAGGACGCGTTTACTACCCTGCCCCGTTTATGACTAACGAGCATCTGGGGCTGt                                                                                                >  1:67092/1‑144 (MQ=255)
                                    aaCCGGTTCTATCTCTTATATCAACCATGCTACGTCGAGTATTCATCCGATTGTGGCGAAAGTAGAGATACGCAAAGAGGGCAAAACATGACGCGTTTACTACCCTGCCCCGTTTATGACTAACGAGAATCTGGCGCTGTATCAGGACg                                                                                       <  2:258162/149‑1 (MQ=255)
                                    aaCCGGTTCTATCTCTTATATCAACCATGCTACGTCGAGTATTCATCCGATTGTGGCGAAAGTAGAGATACGCAAAGAGGGCAAAACAGGACGCGTTTACTACCCTGCCCCGTTTATGACTAACGAGAATCTGGCGCTGTATCAGGACg                                                                                       >  2:179011/1‑149 (MQ=255)
                                             tATCTCTGATAGCAACCCTGCTACTTCGAGTATTCATCCGATTGTGGCGAAAGTAGAGATACGCAAAGAGGGCAAAACAGGACGCGTTTACTACCCTGCCCCGTTTATGACTAACGAGAATCTGGCGCTGTATCAGGACGCTTa                                                                                   <  1:56465/144‑1 (MQ=255)
                                                  ctTATATCAACCATGCTACGTCGAGTATTCATCCGATTGTGGCGAAAGTAGAGATACGCAAAGAGGGCAAAACAGGACGCGTTTACTACCCTGCCCCGTTTATGACTAACGAGAATCTGGCGCTGTATCAGGACGCTTACGAAATTGgc                                                                         >  2:262153/1‑149 (MQ=255)
                                                     atatCAACCATGCTACGTCGAGTATTCATCCGATTGTGGCGAAAGAAGAGATACGCAAAGAGGGCAAAACAGGACGCGTTTACTACCCTGCCCCGTTTATGACTAACGAGAATCTGGCGCTGTATCAGGACGCTTACGAAATTGGCGCa                                                                      >  2:123798/1‑149 (MQ=255)
                                                                 cTACCTCCACTATTCATCCGATTGTGGCAAAAGTAGAGATACGCAAAGAGGGCAAAACAGGACGCGTTTACTACCCTGCCCCGTTTATGACTAACGAGAATCTGTCGCTGTATCAGGACGCTCACGAAATTGGCGCAGAAAAGatcatc                                                          <  2:179440/149‑1 (MQ=255)
                                                                    cGTCGAGTATTCATCCGATTTTGGCGAAAGTAGAGATACGCAAAGAGGGCAAAACAGGACGCGTTTACTACCCTGCCCCGTTTATGACTAATGAGAATCTGGTGCTGTATCAGGACGCTTACGAAATTGGCGCAGAAAAGATCATCGac                                                       <  2:119361/149‑1 (MQ=255)
                                                                                   cGATTGTGGCGAAAGTAGAGATACGCAAAGAGGGCAAAACAGGACGCATTTACTACCCTGCCCCGTTTATGACTAACGAGAATCTGGCGCTGTATCACGAAGCCATCGAAATTGGCGCAGAAAAGATCATCGACACCTACGCGGAAGCg                                        >  2:195102/1‑149 (MQ=255)
                                                                                   cGATTGTGGCGAAAGTAGAGATACGCAAAGAGGGCAAAACAGGACGCATTAACTACCCTGCCCCGTTTATGACTAACGAGAATCTGGCGCTGTATCAGGCAGCAAACGAAATTGACGCCGAAAAGATCATCGACACCTACGCGGAAGCg                                        >  2:195161/1‑149 (MQ=255)
                                                                                             gAAAGTAGAGATACGCAAAGAGGGCAAAACAGGACGCGTTTACTACCCTGCCCCGTTTATGACTAACGAGAATCTGGCGCTGTATCAGGACGCTTACGAAATTGGCGCAGAAAAGATCATCGACACCTACGCGGAAGCGACTCGCCATg                              >  2:213210/1‑149 (MQ=255)
                                                                                                                 agGGCAAAACAGGACGCGTTTACTACCCTGCCCCGTTTATGACTAACGAGAATCTGGCGCTGTATCAGGACGCTTACGAAATTGGCGCAGAAAAGATCATCGACACCTACGCGGAAGCGACTCGCCATGTCGATCAGGGGCTGTCGCTg          <  2:62061/149‑1 (MQ=255)
                                                                                                                       aaaCAGGACGCGTTTACTACCCTGCCCCGTTTATGACTAACGAGAATCTGGCGCTGTATCAGGACGCTTACGAAATTGGCGCAGAAAAGATTATCGACACCTACGCGGAAGCGACCCGCCATGTCGATCAGGGGCTGTCGTTGACGCtt    <  2:197441/149‑1 (MQ=255)
                                                                                                                          cAGGACGCGTTTACTACCCTGCCCCGTTTATGACTAACGAGAATCTGGCGCTGTATCAGGACGCTTACGAAATTGGCGCAGAAAAGATCATCGACACCTACGCGGAAGCGACTCGCCATGTCGATCAGGGGCTGTCGCTGACGc      <  1:161832/144‑1 (MQ=255)
                                                                                                                              aCGCATTTACTATCCTGCCCCGTTTATGACTAACGAGAATCTGGCGCTGTATCAGGACGCTTACGAAATTGGCGCAGAAAAGATCATCGACACCTACGCGGAAGCGACTCGCCATGTCGATCAGGGGCTGTCGCTGACGCtttt  <  1:176968/144‑1 (MQ=255)
                                                                                                                              aCGCATTTACTACCCTGCCCCGTTTATGACTAACGAGAATCTGGCGCTGTATCAGGACGCTTACGAAATTGGCGCAGAAAAGATCATCGACACCTACGCGGAAGCGACTCGCCATGTCGATCAGGGGCTGTCGCTGACGCtttt  <  1:176910/144‑1 (MQ=255)
                                                                                                                                  |                                                                                                                                           
CGGCATATACAACCAGAATCTTCAGGCGGTGCCGCCAACCGGTTCTATCTCTTATATCAACCATGCTACGTCGAGTATTCATCCGATTGTGGCGAAAGTAGAGATACGCAAAGAGGGCAAAACAGGACGCGTTTACTACCCTGCCCCGTTTATGACTAACGAGAATCTGGCGCTGTATCAGGACGCTTACGAAATTGGCGCAGAAAAGATCATCGACACCTACGCGGAAGCGACTCGCCATGTCGATCAGGGGCTGTCGCTGACGCTTTT  >  CP009273/2796434‑2796703

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