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
A6 F28 I1 R1 116 49.4 1663006 99.2% 1649701 139.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,490,764 (C)5→6 coding (66/564 nt) pabA ← aminodeoxychorismate synthase subunit 2

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,490,7591.C95.0% 139.7 / ‑0.0 40coding (71/564 nt)pabAaminodeoxychorismate synthase subunit 2
Reads supporting (aligned to +/- strand):  ref base . (1/1);  new base C (20/18);  total (21/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AATAACGTCAAGGGAGATCCCGGCTTCATCTGGCGTACAGGGGCCAGGTGAGATGACAATTTTTTGTGGTTTAAGGGCGTCGATATCCGCCAGCGTCAACGCATCGTTGCGCTTAACCAGCACATCCG‑C‑CCCCAGTTCACAAAAGTACTGGTAGAGGTTCCAGGTAAAAGAATCGTAGTTATCTATAAGCAGGATCATGGCGGCTCCGGTACAAAAGAACCGCGCTATTTTACTCAGATTCCCCGGCTTCGCTTACCAC  >  NC_000913/3490632‑3490890
                                                                                                                                |                                                                                                                                    
aaTAACGTCAAGGGAGATCCCGGCTTCATCTGGCGTACAGGGGCCAGGTGAGATGACAATTTTTTGTGGTTTAAGGGCGTCGATATCCGCCAGCGTCAACGCATCGTTGCGCTTAACCAGCACATCCGCC‑CCCCAGTTca                                                                                                                          >  1:523417/1‑140 (MQ=255)
    aCGTCAAGGGAGATCCCGGCTTCATCTGGCGTACAGGGGCCAGGTGAGATGACAATTTTTTGTGGTTTAAGGGCGTCGATATCCGCCAGCGTCAACGCATCGTTGCGCTTAACCAGCACATCCGCC‑CCCCAGTTCACaaa                                                                                                                      <  2:762889/140‑1 (MQ=255)
       tCAAGGGAGATCCCGGCTTCATCTGGCGTACAGGGGCCAGGTGAGATGACAATTTTTTGTGGTTTAAGGGCGTCGATATCCGCCAGCGTCAACGCATCGTTGCGCTTAACCAGCACATCCGCC‑CCCCAGTTCACAAAAGt                                                                                                                   <  2:611416/140‑1 (MQ=255)
       tCAAGGGAGATCCCGGCTTCATCTGGCGTACAGGGGCCAGGTGAGATGACAATTTTTTGTGGTTTAAGGGCGTCGATATCCGCCAGCGTCAACGCATCGTTGCGCTTAACCAGCACATCCGCC‑CCCCAGTTCACAAAAGt                                                                                                                   <  1:95202/140‑1 (MQ=255)
                      gCTTCATCTGGCGTACAGGGGCCAGGTGAGATGACAATTTTTTGTGGTTTAAGGGCGTCGATATCCGCCAGCGTCAACGCATCGTTGCGCTTAACCAGCACATCCGCC‑CCCCAGTTCACAAAAGTACTGGTAGAGGTTcc                                                                                                    <  1:363649/140‑1 (MQ=255)
                       cTTCATCTGGCGTACAGGGGCCAGGTGAGATGACAATTTTTTGTGGTTTAAGGGCGTCGATATCCGCCAGCGTCAACGCATCGTTGCGCTTAACCAGCACATCCGCC‑CCCCAGTTCACAAAAGTACTGGTAGAGGTTCCa                                                                                                   >  1:156751/1‑140 (MQ=255)
                       cTTCATCTGGCGTACAGGGGCCAGGTGAGATGACAATTTTTTGTGGTTTAAGGGCGTCGATATCCGCCAGCGTCAACGCATCGTTGCGCTTAACCAGCACATCCG‑C‑CCCCAGGTCACAAAAGGACTTGTAGAGGGTCCAg                                                                                                  >  2:523519/1‑140 (MQ=255)
                           aTCTGGCGTACAGGGGCCAGGTGAGATGACAATTTTTTGTGGTTTAAGGGCGTCGATATCCGCCAGCGTCAACGCATCGTTGCGCTTAACCAGCACATCCGCC‑CCCCAGTTCACAAAAGTACTGGTag                                                                                                           >  1:294654/1‑128 (MQ=255)
                           aTCTGGCGTACAGGGGCCAGGTGAGATGACAATTTTTTGTGGTTTAAGGGCGTCGATATCCGCCAGCGTCAACGCATCGTTGCGCTTAACCAGCACATCCGCC‑CCCCAGTTCACAAAAGTACTGGTag                                                                                                           <  2:294654/128‑1 (MQ=255)
                                 cGTACAGGGGCCAGGTGAGATGACAATTTTTTGTGGTTTAAGGGCGTCGATATCCGCCAGCGTCAACGCATCGTTGCGCTTAACCAGCACATCCGCC‑CCCCAGTTCACAAAAGTACTGGTAGAGGTTCCAGGTAAAAGaa                                                                                         <  1:11311/140‑1 (MQ=255)
                                 cGTACAGGGGCCAGGTGAGATGACAATTTTTTGTGGTTTAAGGGCGTCGATATCCGCCAGCGTCAACGCATCGTTGCGCTTAACCAGCACATCCGCC‑CCCCAGTTCACAAAAGTACTGGTAGAGGTTCCAGGTAAAAGaa                                                                                         >  2:11311/1‑140 (MQ=255)
                                 cGTACAGGGGCCAGGTGAGATGACAATTTTTTGTGGTTTAAGGGCGTCGATATCCGCCAGCGTCAACGCATCGTTGCGCTTAACCAGCACATCCGCC‑CCCCAGTTCACAAAAGTACTGGTAGAGGTTCCAGGTAAAAGaa                                                                                         <  1:514404/140‑1 (MQ=255)
                                  gTACAGGGGCCAGGTGAGATGACAATTTTTTGTGGTTTAAGGGCGTCGATATCCGCCAGCGTCAACGCATCGTTGCGCTTAACCAGCACATCAGCC‑CCCCAGTTCACAAAAGTACTGGTAGAGGTTCCAGGTAAAAGAAt                                                                                        <  1:104658/140‑1 (MQ=255)
                                   tACAGGGGCCAGGTGAGATGACAATTTTTTGTGGTTTAAGGGCGTCGATATCCGCCAGCGTCAACGCATCGTTGCGCTTAACCAGCACATCCGCC‑CCCCAGTTCACAAAAGTACTGGTAGAGGTTCCAGGTAAAAGAATc                                                                                       >  2:451203/1‑140 (MQ=255)
                                        gggCCAGGTGAGATGACAATTTTTTGTGGTTTAAGGGCGTCGATATCCGCCAGCGTCAACGCATCGTTGCGCTTAACCAGCACATCCGCC‑CCCCAGTTCACAAAAGTACTGGTAGAGGTTCCAGGTAAAAGAATCGTAGt                                                                                  <  2:430484/140‑1 (MQ=255)
                                         ggCCAGGTGAGATGACAATTTTTTGTGGTTTAAGGGCGTCGATATCCGCCAGCGTCAACGCATCGTTGCGCTTAACCAGCACATCCGCC‑CCCCAGTTCACAAAAGTACTGGTAGAGGTTCCAGGTAAAAGAATCGTAGtt                                                                                 <  1:620393/140‑1 (MQ=255)
                                          gCCAGGTGAGATGACAATTTTTTGTGGTTTAAGGGCGTCGATATCCGCCAGCGTCAACGCATCGTTGCGCTTAACCAGCACATCCGCC‑CCCCAGTTCACAAAAGTACTGGTAGAGGTTCCAGGTAAAAGAATCGTAGTTa                                                                                >  1:564556/1‑140 (MQ=255)
                                          gCCAGGTGAGATGACAATTTTTTGTGGTTTAAGGGCGTCGATATCCGCCAGCGTCAACGCATCGTTGCGCTTAACCAGCACATCCGCC‑CCCCAGTTCACAAAAGTACTGGTAGAGGTTCCAGGTAAAAGAATCGTAGTTa                                                                                >  2:621510/1‑140 (MQ=255)
                                          gCCAGGTGAGATGACAATTTTTTGTGGTTTAAGGGCGTCGATATCCGCCAGCGTCAACGCATCGTTGCGCTTAACCAGCACATCCGCC‑CCCCAGTTCACAAAAGTACTGGTAGAGGTTCCAGGTAAAAGAATCGTAGTTa                                                                                >  2:417524/1‑140 (MQ=255)
                                             aGGTGAGATGACAATTTTTTGTGGTTTAAGGGCGTCGATATCCGCCAGCGTCAACGCATCGTTGCGCTTAACCAGCACATCCGCC‑CCCCAGTTCACAAAAGTACTGGTAGAGGTTCCAGGTAAAAGAATCGTAGTTATCt                                                                             <  1:278714/140‑1 (MQ=255)
                                                    aTGACAATTTTTTGTGGTTTAAGGGCGTCGATATCCGCCAGCGTCAACGCATCGTTGCGCTTAACCAGCACATCCGCC‑CCCCAGTTCACAAAAGTACTGGTAGAGGTTCCAGGTAAAAGAATCGTAGTTATCTATAAGCa                                                                      >  1:607055/1‑140 (MQ=255)
                                                    aTGACAATTTTTTGTGGTTTAAGGGCGTCGATATCCGCCAGCGTCAACGCATCGTTGCGCTTAACCAGCACATCCGCC‑CCCCAGTTCACAAAAGTACTGGTAGAGGTTCCAGGTAAAAGAATCGTAGTTATCTATAAGCa                                                                      >  2:626740/1‑140 (MQ=255)
                                                    aTGACAATTTTTTGTGGTTTAAGGGCGTCGATATCCGCCAGCGTCAACGCATCGTTGCGCTTAACCAGCACATCCGCC‑CCCCAGTTCACAAAAGTACTGGTAGAGGTTCCAGGTAAAAGAATCGTAGTTATCTATAAGCa                                                                      >  1:808874/1‑140 (MQ=255)
                                                         aaTTTTTTGTGGTTTAAGGGCGTCGATATCCGCCAGCGTCAACGCATCGTTGCGCTTAACCAGCACATCCGCC‑CCCCAGTTCACAAAAGTACTGGTAGAGGTTCCAGGTAAAAGAATCGTAGTTATCTATAAGc                                                                       >  1:396283/1‑134 (MQ=255)
                                                         aaTTTTTTGTGGTTTAAGGGCGTCGATATCCGCCAGCGTCAACGCATCGTTGCGCTTAACCAGCACATCCGCC‑CCCCAGTTCACAAAAGTACTGGTAGAGGTTCCAGGTAAAAGAATCGTAGTTATCTATAAGc                                                                       <  2:396283/134‑1 (MQ=255)
                                                         aaTTTTTTGTGGTTTAAGGGCGTCGATATCCGCCAGCGTCAACGCATCGTTGCGCTTAACCAGCACATCCGCC‑CCCCAGTTCACAAAAGTACTGGTAGAGGTTCCAGGTAAAAGAATCGTAGTTATCTATAAGCAGGATc                                                                 >  2:32709/1‑140 (MQ=255)
                                                             ttttGTGGTTTAAGGGCGTCGATATCCGCCAGCGTAAACGCATCGTTGCGCTTAACCAGCACATCCGCC‑CCCCAGTTCACAAAAGTACTGGTAGAGGGTCCAGGTAAAAGAATCGTAGTTATCTATAAGCAGGATCATgg                                                             >  2:545279/1‑140 (MQ=255)
                                                                   ggTTTAAGGGCGTCGATATCCGCCAGCGTCAACGCATCGTTGCGCTTAACCAGCACATCCGCC‑CCCCAGTTCACAAAAGTACTGGTAGAGGTTCCAGGTAAAAGAATCGTAGTTATCTATAAGCAGGATCATGGCGGCTc                                                       >  2:343450/1‑140 (MQ=255)
                                                                               tCGATATCCGCCAGCGTCAACGCATCGTTGCGCTTAACCAGCACATCCGCC‑CCCCAGTTCACAAAAGTACTGGTAGAGGTTCCAGGTAAAAGAATCGTAGTTATCTATAAGCAGGATCATGGCGGCTCCGGTACAAAAGa                                           >  1:331906/1‑140 (MQ=255)
                                                                                   tatCCGCCAGCGTCAACGCATCGTTGCGCTTAACCAGCACATCCGCC‑CCCCAGTTCACAAAAGTACTGGTAGAGGTTCCAGGTAAAAGAATCGTAGTTATCTATAAGCAGGATCATGGCGGCTCCGGTACAAAAGAACcg                                       <  2:564556/140‑1 (MQ=255)
                                                                                     tCCGCCAGCGTCAACGCATCGTTGCGCTTAACCAGCACATCCGCC‑CCCCAGTTCACAAAAGTACTGGTAGAGGTTCCAGGTAAAAGAATCGTAGTTATCTATAAGCAGGATCATGGCGGCTCCGGTACAAAAGAACcgcg                                     <  2:523417/140‑1 (MQ=255)
                                                                                          cAGCGTCAACGCATCGTTGCGCTTAACCAGCACATCCGCC‑CCCCAGTTCACAAAAGTACTGGTAGAGGTTCCAGGTAAAAGAATCGTAGTTATCTATAAGCAGGATCATGGCGGCTCCGGTACAAAAGAACCGCGCTAtt                                <  1:451203/140‑1 (MQ=255)
                                                                                             cGTCAACGCATCGTTGCGCTTAACCAGCACATCCGCC‑CCCCAGTTCACAAAAGTACTGGTAGAGGTTCCAGGTAAAAGAATCGTAGTTATCTATAAGCAGGATCATGG‑GGCTCCGGTACAAAAGAACCGCGCTATTTTAc                            >  1:752841/1‑140 (MQ=255)
                                                                                                cAACGCATCGTTGCGCTTAACCAGCACATCCGCC‑CCCCAGTTCACAAAAGTACTGGTAGAGGTTCCAGGTAAAAGAATCGTAGTTATCTATAAGCAGGATCATGGCGGCTCCGGTACAAAAGAACCGCGCTATTTTACTc                          <  1:621510/140‑1 (MQ=255)
                                                                                                        cGTTGCGCTTAACCAGCACATCCGCC‑CCCCAGTTCACAAAAGTACTGGTAGAGGTTCCAGGTAAAAGAATCGTAGTTATCTATAAGCAGGATCATGGCGGCTCCGGTACAAAAGAACCGCGCTATTTTACTCAGATTccc                  >  1:395474/1‑140 (MQ=255)
                                                                                                        cGTTGCGCTTAACCAGCACATCCGCC‑CCCCAGTTCACAAAAGTACTGGTAGAGGTTCCAGGTAAAAGAATCGTAGTTATCTATAAGCAGGATCATGGCGGCTCCGGTACAAAAGAACCGCGCTATTTTACTCAGATTccc                  >  1:216402/1‑140 (MQ=255)
                                                                                                             cgcTTAACCAGCACATCCGCC‑CCCCAGTTCACAAAAGTACTGGTAGAGGTTCCAGGTAAAAGAATCGTAGTTATCTATAAGCAGGATCATGGCGGCTCCGGTACAAAAGAACCGCGCTATTTTACTCAGATTCCCCGGCt             <  2:156751/140‑1 (MQ=255)
                                                                                                                    ccAGCACATCCGCC‑CCCCAGTTCACAAAAGTACTGGTAGAGGTTCCAGGTAAAAGAATCGTAGTTATCTATAAGCAGGATCATGGCGGCTCCGGTACAAAAGAACCGCGCTATTTTACTCAGATTCCCCGGCTTCGCTTa      <  1:32709/140‑1 (MQ=255)
                                                                                                                       gCACATCCG‑CTCCCCAGTTCACAAAAGTACTGGTAGAGGTTCCAGGTAAAAGAATCGTAGTTATCTATAAGCAGGATCATGGCGGCTCCGGTACAAAAGAACCGCGCTATTTTACTCAGATTCCCCGGCTTCGCTTACCa   <  1:772775/140‑1 (MQ=255)
                                                                                                                        cacaTCCGCC‑CCCCAGTTCACAAAAGTACTGGTAGAGGTTCCAGGTAAAAGAATCGTAGTTATCTATAAGCAGGATCATGGCGGCTCCGGTACAAAAGAACCGCGCTATTTTACTCAGATTCCCCGGCTTCGCTTACCAc  >  2:337907/1‑140 (MQ=255)
                                                                                                                                |                                                                                                                                    
AATAACGTCAAGGGAGATCCCGGCTTCATCTGGCGTACAGGGGCCAGGTGAGATGACAATTTTTTGTGGTTTAAGGGCGTCGATATCCGCCAGCGTCAACGCATCGTTGCGCTTAACCAGCACATCCG‑C‑CCCCAGTTCACAAAAGTACTGGTAGAGGTTCCAGGTAAAAGAATCGTAGTTATCTATAAGCAGGATCATGGCGGCTCCGGTACAAAAGAACCGCGCTATTTTACTCAGATTCCCCGGCTTCGCTTACCAC  >  NC_000913/3490632‑3490890

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A