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
A11 F56 I1 R1 155 65.2 3164312 95.9% 3034575 99.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,712,306 (T)7→8 intergenic (+148/‑463) nth → / → dtpA DNA glycosylase and apyrimidinic (AP) lyase (endonuclease III)/dipeptide and tripeptide permease A

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,712,2991.T96.2% 183.1 / 0.4 53intergenic (+141/‑470)nth/dtpADNA glycosylase and apyrimidinic (AP) lyase (endonuclease III)/dipeptide and tripeptide permease A
Reads supporting (aligned to +/- strand):  ref base . (1/1);  new base T (22/29);  total (23/30)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.64e-01

ATCCTCTTTTAAAACATCTTTTTAACGTCAATGATGCCATTGCTTAGCGTTATCATCAGGTAATCCGTTTGCGGATAACCAAAAATGCAGGTTAATTG‑TTTTTTTAATAGCGAAATTTTCTATTCATTCGTGATCAAGATCACGATGCTGTCGCAATGTAAAAACATTGCAAGAATCAGGTTAAAATCATT  >  NC_000913/1712202‑1712392
                                                                                                  |                                                                                             
aTCCTCTTTTAAAACATCTTTTTAACGTCAATGATGCCATTGCTTAGCGTTATCATCAGGTAATCCGTTTGCGGATAACCAAAAATGCAGGTTAATTG‑tt                                                                                             >  1:259584/1‑100 (MQ=255)
  ccTCTTTTAAAACATCTTTTTAACGTCAATGATGCCATTGCTTAGCGTTATCATCCGGTAATCCGTTTGCGGATAACCAAAAATGCAGGTTAATTG‑tttt                                                                                           >  2:822473/1‑100 (MQ=255)
   ctctTTTAAAACATCTTTTTAACGTCAATGATGCCATTGCTTAGCGTTATCATCAGGTAATCCGTTTGCGGATAACCAAAAATGCAGGTTAATTG‑ttttt                                                                                          >  2:869507/1‑100 (MQ=255)
      ttttAAAACATCTTTTTAACGTCAATGATGCCATTGCTTAGCGTTATCATCAGGTAATCCGTTTGCGGATAACCAAAAATGCAGGTTAATTG‑tttttttt                                                                                       <  1:550854/100‑2 (MQ=255)
         tAAAACATCTTTTTAACGTCAATGATGCCATTGCTTAGCGTTATCATCAGGTAATCCGTTTGCGGATAACCAAAAATGCAGGTTAATTG‑ttttttttaat                                                                                    >  2:1027558/1‑96 (MQ=255)
          aaaaCATCTTTTTAACGTCAATGATGCCATTGCTTAGCGTTATCATCAGGTAATCCGTTTGCGGATAACCAAAAATGCAGGTTAATTG‑ttttttttaata                                                                                   >  2:461245/1‑95 (MQ=255)
          aaaaCATCTTTTTAACGTCAATGATGCCATTGATTAGCGTTATCATCAGGTAATTCGTTTAAAAAAAAAAAAAAATGCAGGTTAATTG‑TTTTTTTAATAg                                                                                   <  2:225874/100‑1 (MQ=255)
           aaaaATCTTTTTAACGTCAATGATGCCATAGCTTAGCGTTATCATCAGTTAATTTGTTAAAAAAAAAAAAAAAATGCAGGTTAATTGTTTTTTTTAATAg                                                                                   <  2:196546/100‑1 (MQ=255)
            aaCATCTTTTTAACGTCAATGATGCCATTGCTTATCGTTATCATCAGGTAATCCGTTTGCGGATAACCAAAAATGCAGGTTAATTGTTTTTTTTAATAg                                                                                   <  2:434274/99‑1 (MQ=255)
             aCATCTTTTTAACGTCAATGATGCCATTGCTTAGCGTTATCATCAGGTAATCCGTTTGCGGATAACCAAAAATGCAGGTTAATTGTTTTTTTTAATAGCg                                                                                 <  2:180874/100‑1 (MQ=255)
              cATCTTTTTAACGTCAATGATGCCATTGCTTAGCGTTATCATCAGGTAATCCGTTTGCGGATAACCAAAAATGCAGGTTAATTGTTTTTTTTAATAGCGa                                                                                >  2:1201423/1‑100 (MQ=255)
                tCTTTTTAACGTCAATGATGCCATTGCTTAGCGTTATCATCAGGTAATCCGTTTGCGGATAACCAAAAATGCAGGTTAATTG‑tttttttttttttttt                                                                               >  2:153711/1‑89 (MQ=255)
                  tttttAACGTCAATGATGCCATTGCTTAGCGTTATCATCAGGTAATCCGTTTGCGGATAACCAAAAATGCAGGTTAATTGTTTTTTTTAATAGCGAAAtt                                                                            >  2:935993/1‑100 (MQ=255)
                  tttttAACGTCAATGATGCCATTGCTTAGCGTTATCATCAGGTAATCCGTTTGCGGATAACCAAAAATGCAGGTTAATTGTTTTTTTTAATAGCGAAAtt                                                                            >  1:1308558/1‑100 (MQ=255)
                   ttttAACGTCAATGATGCCATTGCTTAGCGTTATCATCAGGTAATCCGTTTGCGGATAACCAAAAATGCAGGTTAATTGTTTTTTTTAATAGCGAAAttt                                                                           <  1:1174590/100‑1 (MQ=255)
                     ttAACGTCAATGATGCCATTGCTTAGCGTTATCATCAGGTAATCCGTTTGCGGATAACCAAAAATGCAGGTTAATTGTTTTTTTTAATAGCGAAATTTTc                                                                         <  2:546360/100‑1 (MQ=255)
                     ttAACGTCAATGATGCCATTGCTTAGCGTTATCATCAGGTAATCCGTTTGCGGATAACCAAAAATGCAGGTTAATTGTTTTTTTTAATAGCGAAATTTTc                                                                         <  2:1487996/100‑1 (MQ=255)
                      tAACGTCAATGATGCCATTGCTTAGCGTTATCATCAGGTAATCCGTTTGCGGATAACCAAAAATGCAGGTTAATTGTTTTTTTTAATAGCGAAATTTTCt                                                                        <  2:84736/100‑1 (MQ=255)
                      tAACGTCAATGATGCCATTGCTTAGCGTTATCATCAGGTAATCCGTTTGCGGATAACCAAAAATGCAGGTTAATTGTTTTTTTTAATAGCGAAATTTTCt                                                                        <  1:362655/100‑1 (MQ=255)
                       aaCGTCAATGATGCCATTGCTTAGCGTTATCATCAGGTAATCCGTTTGCGGATAACCAAAAATGCAGGTTAATTG‑TTTTTTTAATAGCGAAATTTTCTat                                                                      >  2:988264/1‑100 (MQ=255)
                          gTCAATGATGCCATTGCTTAGCGTTATCATCAGGTAATCCGTTTGCGGATAACCAAAAATGCAGGTTAATTGTTTTTTTTAATAGCGAAATTTTCTattc                                                                    <  2:36791/100‑1 (MQ=255)
                               tgatgCCATTGCTTAGCGTTATCATCAGGTAATCCGTTTGCGGATAACCAAAAATGCAGGTTAATTGTTTTTTTTAATAGCGAAATTTTCTATTCATTCg                                                               >  2:13760/1‑100 (MQ=255)
                                 atacaagtGCTTAGCGGTATCATGAGGTAATCAGTTGACGGATAACAAAAAATGCAGGTTAATTGTTTTTTTTAATAGCGAAATTTTCTATTCATTCg                                                               <  2:650890/91‑1 (MQ=255)
                                   gCCATTGCTTAGCGTTATCATCAGGTAATCCGTTTGCGGATAACCAAAAATGCAGGTTAATTGTTTTTTTTAATAGCGAAATTTTCTATTCATTCGTGAt                                                           >  1:1389265/1‑100 (MQ=255)
                                    ccATTGCTTAGCGTTATCATCAGGTAATCCGTTTGCGGATAACCAAAAATGCAGGTTAATTGTTTTTTTTAATAGCGAAATTTTCTATTCATTCGTGATc                                                          <  1:471764/100‑1 (MQ=255)
                                        tGCTTAGCGTTATCATCAGGTAATCCGTTTGCGGATAACCAAAAATGCAGGTTAATTGTTTTTTTTAATAGCGAAATTTTCTATTCATTCGTGATCAAGa                                                      >  2:492539/1‑100 (MQ=255)
                                          cTTAGCGTTATCATCAGGTAATCCGTTTGCGGATAACCAAAAATGCAGGTTAATTGTTTTTTTTAATAGCGAAATTTTCTATTCGTTCGTGATCAAGATc                                                    >  1:1554340/1‑100 (MQ=255)
                                          cTTAGCGTTATCATCAGGTAATCCGTTTGCGGATAACCAAAAATGCAGGTTAATTGTTTTTTTTAATAGCGAAATTTTCTATTCATTCGTGATCAAGAt                                                     <  1:1201428/99‑1 (MQ=255)
                                           ttAGCGTTATCATCAGGTAATCCGTTTGCGGATAACCAAAAATGCAGGTTAATTGTTTTTTTTAATAGCGAAATTTTCTATTCATTCGTGATCAAGATCa                                                   >  2:675938/1‑100 (MQ=255)
                                            tAGCGTTATCATCAGGTAATCCGTTTGCGGATAACCAAAAATGCAGGTTAATTGTTTTTTTTAATAGCGAAATTTTCTATTCATTCGTGATCAAGATCAc                                                  >  1:186626/1‑100 (MQ=255)
                                              gCGTTATCATCAGGTAATCCGTTTGCGGATAACCAAAAATGCAGGTTAATTGTTTTTTTTAATAGCGAAATTTTCTATTCATTCGTGATCAAGATCACGa                                                <  1:1172048/100‑1 (MQ=255)
                                               cGTTATCATCAGGTAATCCGTTTGCGGATAACCAAAAATGCAGGTTAATTGTTTTTTTTAATAGCGAAATTTTCTATTCATTCGTGATCAAGATCACGAt                                               <  1:13760/100‑1 (MQ=255)
                                                   atcatcAGGTAATCCGTTTGCGGATAACCAAAAATGCAGGTTAATTGTTTTTTTTAATAGCGAAATTTTCTATTCATTCGTGATCAAGATCACGATGCt                                            >  2:1454880/1‑99 (MQ=255)
                                                    tcatcaGGTAATCCGTTTGCGGATAACCAAAAATGCAGGTTAATTGTTTTTTTTAATAGCGAAATTTTCTATTCATTCGTGATCAAGATCACGATGCTGt                                          <  2:658839/100‑1 (MQ=255)
                                                      atcaGGTAATCCGTTTGCGGATAACCAAAAATGCAGGTTAATTGTTTTTTTTAATAGCGAAATTTTCTATTCATTCGTGATCAAGATCACGATGCTGTCg                                        >  1:287059/1‑100 (MQ=255)
                                                       tcaGGTAATCCGTTTGCGGATAACCAAAAATGCAGGTTAATTGTTTTTTTTTTTTTTTTTATTTTCTATTCATTCGTGATCAAGATCACGATGCTGTCGc                                       >  2:218221/1‑100 (MQ=255)
                                                          ggTAATCCGTTTGCGGATAACCAAAAATGCAGGTTAATTGTTTTTTTTAATAGCGAAATTTTCTATTCATTCGTGATCAAGATCACGATGCTGTCGCAAt                                    <  1:913519/100‑1 (MQ=255)
                                                           gTAATCCGTTTGCGGATAACCAAAAATGCAGGTTAATTGTTTTTTTTAATAGCGAAATTTTCTATTCATTCGTGATCAAGATCACGATGCTGTCGCAATg                                   <  1:123131/100‑1 (MQ=255)
                                                            tAATCCGTTTGCGGATAACCAAAACTGCAGGTTAATTGTTTTTTTTAATAGCGAAATTTTCTATTCATTCGTGATCAAGATCACGATGCTGTCGCAATg                                   <  2:1027381/99‑1 (MQ=255)
                                                            tAATCCGTTTGCGGATAACCAAAAATGCAGGTTAATTGTTTTTTTTAATAGCGAAATTTTCTATTCATTCGTGATCAAGATCACGATGCTGTCGCAATGt                                  >  2:1070280/1‑100 (MQ=255)
                                                                ccGTTTGCGGATAACCAAAAATGCAGGTTAATTGTTTTTTTTAATAGCGAAATTTTCTATTCATTCGTGATCAAGATCACGATGCTGTCGCAATGTaaaa                              <  1:1229912/100‑1 (MQ=255)
                                                                     tGCGGATAACCAAAAATGCAGGTTAATTGTTTTTTTTAATAGCGAAATTTTCTATTCATTCGTGATCAAGATCACGATGCTGTCGCAATGTAAAAACAtt                         >  1:1372680/1‑100 (MQ=255)
                                                                      gCGGATAACCAAAAATGCAGGTTAATTGTTTTTTTTAATAGCGAAATTTTCTATTCATTCGTGATCAAGATCACGATGCTGTCGCAATGTAAAAACATTg                        >  1:1182304/1‑100 (MQ=255)
                                                                       cGGATAACCAAAAATGCAGGTTAATTGTTTTTTTTAATAGCGAAATTTTCTATTCATTCGTGATCAAGATCACGATGCTGTCGCAATGTAAAAACATTGc                       >  1:1395465/1‑100 (MQ=255)
                                                                       cGGATAACCAAAAATGCAGGTTAATTGTTTTTTTTAATAGCGAAATTTTCTATTCATTCGTGATCAAGATCACGATGCTGTCGCAATGTAAAAACATTGc                       <  1:218221/100‑1 (MQ=255)
                                                                         gATAACCAAAAATGCAGGTTAATTGTTTTTTTTAATAGCGAAATTTTCTATTCATTCGTGATCAAGATCACGATGCTGTCGCAATGTAAAAACATTGCaa                     <  1:869512/100‑1 (MQ=255)
                                                                          aTAACCAAAAATGCAGGTTAATTGTTTTTTTTAATAGCGAAATTTTCTATTCATTCGTGATCAAGATCACGATGCTGTCGCAATGTAAAAACATTGCa                      <  2:882173/98‑1 (MQ=255)
                                                                             aCCAAAAATGCAGGTTAATTGTTTTTTTTAATAGCGAAATTTTCTATTCATTCGTGATCAAGATCACGATGCTGTCGCAATGTAAAAACATTGCAAGAAt                 >  1:1528666/1‑100 (MQ=255)
                                                                               cAAAAATGCAGGTTAATTGTTTTTTTTTTTTTTTTTATTTTCTATTCATTCGTGATCAAGATCATGTTGCTGTCGCAATGTAAAAACATTGTAAGAAt                 >  2:1170077/1‑98 (MQ=255)
                                                                               cAAAAATGCAGGTTAATTGTTTTTTTTAATAGCGAAATTTTCTATTCATTCGTGATCAAGATCACGATGCTGTCGCAATGTAAAAACATTGCAAGAATCa               >  1:1039092/1‑100 (MQ=255)
                                                                                 aaaaTGCAGGTTAATTGTTTTTTTTAATAGCGAAATTTTCTATTCATTCGTGATCAAGATCACGATGCTGTCGCAATGTAAAAACATTGCAAGAATCAgg             <  1:375774/100‑1 (MQ=255)
                                                                                 aaaaTGCAGGTTAATTGTTTTTTTTAATAGCGAAATTTTCTATTCATTCGTGATCAAGATCACGATGCTGTCGCAATGTAAAAACATTGCAAGAATCAgg             <  1:822478/100‑1 (MQ=255)
                                                                                 aaaaTGCAGGTTAATTGTTTTTTTTAATAGCGAAATTTTCTATTCATTCGTGATCAAGATCACGATGCTGTCGCAATGTAAAAACATTGCAAGAATCAgg             <  2:342533/100‑1 (MQ=255)
                                                                                 aaaaTGCAGGTTAATCGTTTTTTTTAATAGCGAAATTTTCTATTCATTCGTGATCAAGATCACGATGCTGTCGCAATGTAAAAACATTGCAAGAATCAgg             <  1:1557332/100‑1 (MQ=255)
                                                                                   aaTGCAGGTTAATTGTTTTTTTTAATAGCGAAATTTTCTATTCATTCGTGATCAAGATCACGATGCTGTCGCAATGTAAAAACATTGCAAGAATCAGGtt           <  1:451348/100‑1 (MQ=255)
                                                                                       cAGGTTAATTGTTTTTTTTAATAGCGAAATTTTCTATTCATTCGTGATCAAGATCACGATGCTGTCGCAATGTAAAAACATTGCAAGAATCAGGTTaaaa       >  2:1152694/1‑100 (MQ=255)
                                                                                        aGGTTAATTGTTTTTTTTAATAGCGAAATTTTCTATTCATTCGTGATCAAGATCACGATGCTGTCGCAATGTAAAAACATTGCAAGAATCAGGTTAAAAt      <  2:578716/100‑1 (MQ=255)
                                                                                         ggTTAATTGTTTTTTTTAATAGCGAAATTTTCTATTCATTCGTGATCAAGATCACGATGCTGTCGCAATGTAAAAACATTGCAAGAATCAGGTTAAAATc     >  1:287756/1‑100 (MQ=255)
                                                                                          gTTAATTGTTTTTTTTAATAGCGAAATTTTCTATTCATTCGTGATCAAGATCACGATGCTGTCGCAATGTAAAAACATTGCAAGAATCAGGTTAAAATCa    >  1:463972/1‑100 (MQ=255)
                                                                                            tAATTGTTTTTTTTAATAGCGAAATTTTCTATTCATTCGTGATCAAGATCACGATGCTGTCGCAATGTAAAAACATTGCAAGAATCAGGTTAAAATCAtt  <  1:1128621/100‑1 (MQ=255)
                                                                                                  |                                                                                             
ATCCTCTTTTAAAACATCTTTTTAACGTCAATGATGCCATTGCTTAGCGTTATCATCAGGTAATCCGTTTGCGGATAACCAAAAATGCAGGTTAATTG‑TTTTTTTAATAGCGAAATTTTCTATTCATTCGTGATCAAGATCACGATGCTGTCGCAATGTAAAAACATTGCAAGAATCAGGTTAAAATCATT  >  NC_000913/1712202‑1712392

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A