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
A10 F112 I1 R1 17 70.3 3408026 96.6% 3292153 99.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,248,180 A→C R136S (AGA→AGC)  yqjA → general envelope maintenance protein; DedA family inner membrane protein; putative multidrug efflux transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,248,1800AC93.5% 208.8 / 3.6 62R136S (AGA→AGC) yqjAgeneral envelope maintenance protein; DedA family inner membrane protein; putative multidrug efflux transporter
Reads supporting (aligned to +/- strand):  ref base A (2/2);  new base C (33/25);  total (35/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.46e-01

ATTTACCCGCGCATTATCATCAACGCGCACACCATCTTTTTCATAAACACGGTTTATCGGCGCTGTTAATTGGTCGCTTTATTGCGTTTGTCAGAACACTGCTGCCGACGATTGCCGGGTTATCAGGGCTGAATAACGCGCGCTTTCAGTTTTTCAACTGGATGAGCGGTCTGCTGTGGGTATTGATCCTG  >  NC_000913/3248086‑3248276
                                                                                              |                                                                                                
acttACCCGCGCATTATCATCAACGCGCACACCATCTTTTTCATAAACACGGTTTATCGGCGCTGTTAATTGGTCGCTTTATTGCGTTTGTCAGAACAct                                                                                             <  2:1367242/98‑1 (MQ=255)
     cccGCGCATTATCATCAACGCGCACACCATCTTTTTCATAAACACGGTTTATCGGCGCTGTTAATTGGTCGCTTTATTGCGTTTGTCAGCACACtgctgc                                                                                        >  2:969251/1‑100 (MQ=255)
      ccGCGCATTATCATCAACGCGCACACCATCTTTTTCATAAACACGGTTTATCGGCGCTGTTAATTGGTCGCTTTATTGCGTTTGTCAGCACACTGCTGcc                                                                                       <  1:660510/100‑1 (MQ=255)
      ccGCGCATTATCATCAACGCGCACACCATCTTTTTCATAAACACGGTTTATCGGCGCTGTTAATTGGTCGCTTTATTGCGTTTGTCAGCACACTGCTGcc                                                                                       <  1:1386358/100‑1 (MQ=255)
        gcgcATTATCATCAACGCGCACACCATCTTTTTCATAAACACGGTTTATCGGCGCTGTTAATTGGTCGCTTTATTGCGTTTGTCAGCACACTGCTGCcga                                                                                     >  1:1546810/1‑100 (MQ=255)
           cactATCATCAACGCGCACACCATCTTTTTCATAAACACGGTTTATCGGCGCTGTTAATTGGTCGCTTTATTGCGTTTGTCAGCACACTGCTGCcgacga                                                                                  >  2:559875/4‑100 (MQ=255)
           cATTCTCATCCACGCGCACACCATCTTTTTCGTAAACAGGGTTTATCGGAGATGTTAATTCGTGGCTGTCTTGCGTTTGTCCGCACTCTGCTGcc                                                                                       >  1:762309/1‑95 (MQ=255)
           cATTATCATCAACGCGCACACCATCTTTTTCATAAACACGGTTTATCGGCGCTGTTAATTGGTCGCTTTATTGCGTTTGTCAGCACACTGCTGCcgacga                                                                                  >  2:913489/1‑100 (MQ=255)
              tATCATCAACGCGCACACCATCTTTTTCATAAACACGGTTTATCGGCGCTGTTAATTGGTCGCTTTATTGCGTTTGTCAGAACACTGCTGCCGACGATTg                                                                               <  1:1142900/100‑1 (MQ=255)
                    caACGCGCACACCATCTTTTTCATAAACACGGTTTATCGGCGCTGTTAATTGGTCGCTTTATTGCGTTTGTCAGCACACTGCTGCCGACGATTGCCggg                                                                          >  1:441106/1‑99 (MQ=255)
                    caACGCGCACACCATCTTTTTCATAAACACGGTTTATCGGCGCTGTTAATTGGTCGCTTTATTGCGTTTGTCAGCACACTGCTGCCGACGATTGCCGGGt                                                                         >  1:602295/1‑100 (MQ=255)
                     aaCGCGCACACCATCTTTTTCATAAACACGGTTTATCGGCGCTGTTAATTGGTCGCTTTATTGCGTTTGTCAGCACACTGCTGCCGACGATTGCCGGGtt                                                                        >  1:1406664/1‑100 (MQ=255)
                     aaCGCGCACACCATCTTTTTCATAAACACGGTTTATCGGCGCTGTTAATTGGTCGCTTTATTGCGTTTGTCAGCACACTGCTGCCGACGATTGCCGGGtt                                                                        <  1:328676/100‑1 (MQ=255)
                      aCGCGCACACCATCTTTTTCATAAACACGGTTTATCGGCGCTGTTAATTGGTCGCTTTATTGCGTTTGTCAGCACACTGCTGCCGACGATTGCCGGGTTa                                                                       <  2:559667/100‑1 (MQ=255)
                          gcACACCATCTTTTTCATAAACACGGTTTATCGGCGCTGTTAATTGGTCGCTTTATTGCGTTTGTCAGCACACTGCTGCCGACGATTGCCGGGTTATCAg                                                                   >  2:822868/1‑100 (MQ=255)
                           cacaCCATCTTTTTCATAAACACGGTTTATCGGCGCTGTTAATTGGTCGCTTTATTGCGTTTGTCAGCACACTGCTGCCGACGATTGCCGGGTTATCAgg                                                                  <  1:1080294/100‑1 (MQ=255)
                             cacCATCTTTTTCATAAACACGGTTTATCGGCGCTGTTAATTGGTCGCTTTATTGCGTTTGTCAGCACACTGCTGCCGACGATTGCCGGGTTATCAGGGc                                                                >  2:1284272/1‑100 (MQ=255)
                              acCATCTTTTTCATAAACACGGTTTATCGGCGCTGTTAATTGGTCGCTTTATTGCGTTTGTCAGCACACTGCTGCCGACGATTGCCGGGTTATCAGGGCt                                                               >  1:1359737/1‑100 (MQ=255)
                                cATCTTTTTCATAAACACGGTTTATCGGCGCTGTTAATTGGTCGCTTTATTGCGTTTGTCAGCACACTGCTGCCGACGATTGCCGGGTTATCAGGGCTGa                                                             <  2:1469381/100‑1 (MQ=255)
                                 aTCTTTTTCATAAACACGGTTTATCGGCGCTGTTAATTGGTCGCTTTATTGCGTTTGTCAGCACACTGCTGCCGACGATTGCCGGGTTATCAGGGCTGaa                                                            >  1:508114/1‑100 (MQ=255)
                                  tCTTTTTCATAAACACGGTTTATCGGCGCTGTTAATTGGTCGCTTTATTGCGTTTGTCAGCACACTGCTGCCGACGATTGCCGGGTTATCAGGGCTGAAt                                                           >  1:684700/1‑100 (MQ=255)
                                     ttttCATAAACACGGTTTATCGGCGCTGTTAATTGGTCGCTTTATTGCGTTTGTCAGCACACTGCTGCCGACGATTGCCGGGTTATCAGGGCTGAATAAc                                                        <  2:371542/100‑1 (MQ=255)
                                       ttCTTAAACACGGTTTATCGGCGCTGTTAATTGGTCGCTTTATTGCGTTTGTCAGCACACTGCTGCCGTCGATTGTCGGGTTATCAGGGCTGAATAAcg                                                       <  1:755040/99‑1 (MQ=255)
                                       ttCATAAACACGGTTTATCGGCGCTGTTAATTGGTCGCTTTATTGCGTTTGTCAGCACACTGCTGCCGACGATTGCCGGGTTATCAGGGCTGAATAAcgc                                                      >  1:408862/1‑100 (MQ=255)
                                          aTAAACACGGTTTATCGGCGCTGTTAATTGGTCGCTTTATTGCGTTTGTCAGCACACTGCTGCCGACGATTGCCGGGTTATCAGGGCTGAATAAcgcgcg                                                   >  2:996124/1‑100 (MQ=255)
                                            aaaCACGGTTTATCGGCGCTGTTAATTGGTCGCTTTATTGCGTTTGTCAGCACACTGCTGCCGACGATTGCCGGGTTATCAGGGCTGAATAACGCGCGCt                                                 >  2:855880/1‑100 (MQ=255)
                                             aaCACGGTTTATCGGCGCTGTTAATTGGTCGCTTTATTGCGTTTGTCAGCACACTGCTGCCGACGATTGCCGGGTTATCAGGGCTGAATAACGCGCGCtt                                                >  2:1564591/1‑100 (MQ=255)
                                             aaCACGGTTTATCGGCGCTGTTAATTGGTCGCTTTATTGCGTTTGTCAGCACACTGCTGCCGACGATTGCCGGGTTATCAGGGCTGAATAACGCGCGCtt                                                <  2:484762/100‑1 (MQ=255)
                                             aaCACGGTTTATCGGCGCTGTTAATTGGTCGCTTTATTGCGTTTGTCAGCACACTGCTGCCGACGATTGCCGGGTTATCAGGGCTGAATAACGCGCGCt                                                 >  1:1536333/1‑99 (MQ=255)
                                               cacGGTTTATCGGCGCCGTTAATTGGTCGCTTTATTGCGTTTGTCAGCACACTGCTGCCGACGATTGCCGGGTTATCAGGGCTGAATAACGCGCGCTTTc                                              <  1:996120/100‑1 (MQ=255)
                                                 cGGTTTATCGGCGCTGTTAATTGGTCGCTTTATTGCGTTTGTCAGCACACTGCTGCCGACGATTGCCGGGTTATCAGGGCTGAATAACGCGCGCTTTCAg                                            >  2:1016627/1‑100 (MQ=255)
                                                  ggTTTATCGGCGCTGTTAATTGGTCGCTTTATTGCGTTTGTCAGCACACTGCTGCCGACGATTGCCGGGTTATCAGGGCTGAATAACGCGCGCTTTCAGt                                           >  2:872291/1‑100 (MQ=255)
                                                   gTTTATCGGCGCTGTTAATTGGTCGCTTTATTGCGTTTGTCAGCACACTGCTGCCGACGATTGCCGGGTTATCAGGGCTGAATAACGCGCGCTTTCAGtt                                          <  1:1284266/100‑1 (MQ=255)
                                                     ttATCGGCGCTGTTAATTGGTCGCTTTATTGCGTTTGTCAGCACACTGCTGCCGACGATTGCCGGGTTATCAGGGCTGAATAACGCGCGCTTTCAGtttt                                        <  1:840175/100‑1 (MQ=255)
                                                       aTCGGCGCTGTTAATTGGTCGCTTTATTGCGTTTGTCAGCACACTGCTGCCGACGATTGCCGGGTTATCAGGGCTGAATAACGCGCGCTTTCAGTTTTTc                                      <  1:1562303/100‑1 (MQ=255)
                                                        tCGGCGCTGTTAATTGGTCGCTTTATTGCGTTTGTCAGCACACTGCTGCCGACGATTGCCGGGTTATCAGGGCTGAATAACGCGCGCTTTCAGTTTTTCa                                     <  2:37205/100‑1 (MQ=255)
                                                        tCGGCGCTGTTAATTGGTCGCTTTATTGCGTTTGTCAGCACACTGCTGCCGACGATTGCCGGGTTATCAGGGCTGAATAACGCGCGCTTTCAGTTTTTCa                                     <  1:1061804/100‑1 (MQ=255)
                                                          gccgcTGTTAAATGGTCGCTTTATTGCGGGTGGCAGCACACTACTTCCTACGATGGCCGGGTTATCAGGGCTGAATAACGCTCGCTTTCAGTGTTTCAAc                                   >  1:992581/3‑100 (MQ=255)
                                                            cgcTGTTAATCGGTCGCTTTGTTGGGTTTGTTATCATACTTCGTCCGTCGATTGCCTGGTTATCAGGGCTGAATAGCCCAGGTTTTTAGTTTTTCAACTg                                 <  1:990248/100‑1 (MQ=255)
                                                              cTGTTAATTGGTCGCTTTATTGCGTTTGTCAGCACACTGCTGCCGACGATTGCCGGGTTATCAGGGCTGAATAACGCGCGCTTTCAGTTTTTCAACTGGa                               <  2:423361/100‑1 (MQ=255)
                                                                gTTAATTGGTCGCTTTATTGCGTTTGTCAGCACACTGCTGCCGACGATTGCCGGGTTATCAGGGCTGAATAACGCGCGCTTTCAGTTTTTCAACTGGATg                             >  2:789500/1‑100 (MQ=255)
                                                                  gatctGGTCGCTTTATTGCGTTTGTCAGCACACTGCTGCCGACGATTGCCGGGTTATCAGGGCTGAATAACGCGCGCTTTCAGTTTTTCAACTGGATGAg                           <  2:1348877/96‑1 (MQ=255)
                                                                   gaTTGGTCGCTTTATTGCGTTTGTCAGAACACTGCTGCCGACGATTGCCGGGTTATCAGGGCTGAATAACGCGCGCTTTCAGTTTTTCACCTGGATGAGc                          >  1:283696/2‑100 (MQ=255)
                                                                   aaTTGGTCGCTTTATTGCGTTTGTCAGCACACTGCTGCCGACGATTGCCGGGTTATCAGGGCTGAATAACGCGCGCTTTCAGTTTTTCAACTGGATGAGc                          >  2:29413/1‑100 (MQ=255)
                                                                    aTTGGTCGCTTTATTGCGTTTGTCAGCACACTGCTGCCGACGATTGCCGGGTTATCAGGGCTGAATAACGCGCGCTTTCAGTTTTTCAACTGGATGAGCg                         <  2:761738/100‑1 (MQ=255)
                                                                      tGGTCGCTTTATTGCGTTTGTCAGCACACTGCGGCCGACGATTGCCGGGTTATCAGGGCTGAATAACGCGCGCTTTCAGTTTTTCAACTGGATGAGCgg                        <  1:1535470/99‑1 (MQ=255)
                                                                       ggTCGCTTTATTGCGTTTGTCAGCACACTGCTGCCGACGATTGCCGGGTTATCAGGGCTGCATAACGCGCGCTTTCAGTTTTTCAACTGGATGCGCGGTc                      >  1:63060/1‑100 (MQ=255)
                                                                       ggTCGCTTTATTGCGTTTGTCAGCACACTGCTGCCGACGATTGCCGGGTTATCAGGGCTGAATAACGCGCGCTTTCAGTTTTTCAACTGGATGAgagatc                      >  1:1348871/1‑95 (MQ=255)
                                                                        gTCGCTTTATTGCGTTTGTCAGCACACTGCTGCCGACGATTGCCGGGTTATCAGGGCTGAATAACGCGCGCTTTCAGTTTTTCAACTGGATGAGCGGTct                     >  2:1344897/1‑100 (MQ=255)
                                                                        gTCGCTTTATTGCGTTTGTCAGCACACTGCTGCCGACGATTGCCGGGTTATCAGGGCTGAATAACGCGCGCTTTCAGTTTTTCAACTGGATGAGCGGTct                     >  1:1080538/1‑100 (MQ=255)
                                                                           gCTTTATTGCGTTTGTCAGCACACTGCTGCCGACGATTGCCGGGTTATCAGGGCTGAATAACGCGCGCTTTCAGTTTTTCAACTGGATGAGCGGTctgct                  >  1:1270772/1‑100 (MQ=255)
                                                                               tATTGCGTTTGTCAGCACACTGCTGCCGACGATTGCCGGGTTATCAGGGCTGAATAACGCGCGCTTTCAGTTTTTAAACCGGATGAGCGGTCTGCTGTgg              <  1:76845/100‑1 (MQ=255)
                                                                                  tGCGTTTGTCAGCACACTGCTGCCGACGATTGCCGGGTTATCAGGGCTGAATAACGCGCGCTTTCAGTTTTTCAACTGGATGAGCGGTCTGCTGTGGGTa           >  2:866604/1‑100 (MQ=255)
                                                                                  tGCGTTTGTCAGCACACTGCTGCCGACGATTGCCGGGTTATCAGGGCTGAATAACGCGCGCTTTCAGTTTTTCAACTGGATGAGCGGTCTGCTGTGGGTa           >  1:584438/1‑100 (MQ=255)
                                                                                   gCGTTTGTCAGCACACTGCTGCCGACGATTGCCGGGTTATCAGGGCTGAATAACGCGCGCTTTCAGTTTTTCAACTGGATGAGCGGTCTGCTGTGGGTAt          >  1:1550366/1‑100 (MQ=255)
                                                                                   gCGTTTGTCAGCACACTGCTGCCGACGATTGCCGGGTTATCAGGGCTGAATAACGCGCGCTTTCAGTTTTTCAACTGGATGAGCGGTCTGCTGTGGGTAt          <  1:373407/100‑1 (MQ=255)
                                                                                    cGTTTGTCAGCACACTGCTGCCGACGATTGCCGGGTTATCAGGGCTGAATAACGCGCGCTTTCAGTTTTTCAACTGGATGAGCGGTCTGCTGTGGGTAtt         <  2:1546817/100‑1 (MQ=255)
                                                                                     gTTTGTCAGCACACTGCTGCCAACGATTGCCGGGTTATCAGGACTGAATAACGCGCGCTTTAAGTTTTTCAACTGGATGAGCGGTCTACTGTGGGTAtt         >  1:1447511/1‑99 (MQ=255)
                                                                                      tttGTCAGCACACTGCTGCCGACGATTGCCGGGTTATCAGGGCTGAATAACGCGCGCTTTCAGTTTTTCAACTGGATGAGCGGTCTGCTGTGGGTATTGa       <  2:1080544/100‑1 (MQ=255)
                                                                                          tCAGCACACTGCTGCCGACGATTGCCGGGTTATCAGGGCTGAATAACGCGCGCTTTCAGTTTTTCAACTGGATGAGCGGTCTGCTGTGGGTATTGATCCt   <  1:866602/100‑1 (MQ=255)
                                                                                           cAGCACACTGCTGCCGACGATTGCCGGGTTATCAGGGCTGAATAACGCGCGCTTTCAGTTTTTCAACTGGATGAGCGGTCTGCTGTGGGTCTTGATCCTg  >  1:1350576/1‑100 (MQ=255)
                                                                                           cAGAACACTGCTGCCGACGATTGCCGGGTTATCAGGGCTGAATAACGCGCGCTTTCAGTTTTTCAACTGGATGAGCGGTCTGCTGTGGGTATTGATCCTg  >  2:598030/1‑100 (MQ=255)
                                                                                              |                                                                                                
ATTTACCCGCGCATTATCATCAACGCGCACACCATCTTTTTCATAAACACGGTTTATCGGCGCTGTTAATTGGTCGCTTTATTGCGTTTGTCAGAACACTGCTGCCGACGATTGCCGGGTTATCAGGGCTGAATAACGCGCGCTTTCAGTTTTTCAACTGGATGAGCGGTCTGCTGTGGGTATTGATCCTG  >  NC_000913/3248086‑3248276

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A