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
A1 F17 I0 R2 276 45.3 3729697 93.0% 3468618 60.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 3,518,471 T→C 11.2% intergenic (‑305/‑120) yiiU ← / → glpF conserved hypothetical protein/glycerol facilitator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,518,4710TC11.2% 212.5 / 16.9 80intergenic (‑305/‑120)yiiU/glpFconserved hypothetical protein/glycerol facilitator
Reads supporting (aligned to +/- strand):  ref base T (37/34);  new base C (4/5);  total (41/39)
Fisher's exact test for biased strand distribution p-value = 7.34e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CATCATGTACAATCAGATGGAATAAATGGCGCGATAACGCTCATTTTATGACGAGGCACACACATTTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTACAGCATGCCTACAAGCATCGTG  >  W3110S.gb/3518406‑3518537
                                                                 |                                                                  
catcatGTACAATCAGATGGAATAAATGGCGCGATAACGCTCATTTTATGACGAGGCACACACATTTTa                                                                 <  1:1487405/69‑1 (MQ=255)
    atGTACAATCAGATGGAATAAATGGCGCGATAACGCTCATTTTATGACGAGGCACACACATTTTAAGt                                                              >  1:717955/1‑68 (MQ=255)
    atGTACAATCAGATGGAATAAATGGCGCGATAACGCTCATTTTATGACGAGGCACACACATTTTAAGt                                                              >  1:2073095/1‑68 (MQ=255)
    atGTACAATCAGATGGAATAAATGGCGCGATAACGCTCATTTTATGACGAGGCACACACATTTTAAGt                                                              >  1:1851771/1‑68 (MQ=255)
    atGTACAATCAGATGGAATAAATGGCGCGATAACGCTCATTTTATGACGAGGCACACACATTTTAAGt                                                              >  1:2792278/1‑68 (MQ=255)
     tGTACAATCAGATGGAATAAATGGCGCGATAACGCTCATTTTATGACGAGGCACACACATTTTAAGTTc                                                            >  1:2514934/1‑69 (MQ=255)
     tGTACAATCAGATGGAATAAATGGCGCGATAACGCTCATTTTATGACGAGGCACACACATTTTAAGTTc                                                            >  1:188591/1‑69 (MQ=255)
       tACAATCAGATGGAATAAATGGCGCGATAACGCTCATTTTATGACGAGGCACACACAtttt                                                                  <  1:1050408/61‑1 (MQ=255)
       tACAATCAGATGGAATAAATGGCGCGATAACGCTCATTTTATGACGAGGCACACACAtttt                                                                  >  1:402273/1‑61 (MQ=255)
       tACAATCAGATGGAATAAATGGCGCGATAACGCTCATTTTATGACGAGGCACACACAtttt                                                                  >  1:2590116/1‑61 (MQ=255)
       tACAATCAGATGGAATAAATGGCGCGATAACGCTCATTTTATGACGAGGCACACACATTTTAAGTTCGa                                                          >  1:2379721/1‑69 (MQ=255)
       tACAATCAGATGGAATAAATGGCGCGATAACGCTCATTTTATGACGAGGCACACACATTTTAAGTTCGa                                                          >  1:1134715/1‑69 (MQ=255)
       tACAATCAGATGGAATAAATGGCGCGATAACGCTCATTTTATGACGAGGCACACACATTTTAAGTTCGa                                                          >  1:715585/1‑69 (MQ=255)
       tACAATCAGATGGAATAAATGGCGCGATAACGCTCATTTTATGACGAGGCACACACATTTTAAGTTCGa                                                          >  1:577017/1‑69 (MQ=255)
       tACAATCAGATGGAATAAATGGCGCGATAACGCTCATTTTATGACGAGGCACACACATTTTAAGTTCGa                                                          >  1:1768155/1‑69 (MQ=255)
       tACAATAAGATGGAATAAATGGCGCGATAACGCTCATTTTATGACGAGGCACACACAtttt                                                                  >  1:2299321/1‑61 (MQ=255)
        aCAATCAGATGGAATAAATGGCGCGATAACGCTCATTTTATGACGAGGCACACACATTTTAAGTTCGat                                                         >  1:2705293/1‑69 (MQ=255)
        aCAATCAGATGGAATAAATGGCGCGATAACGCTCATTTTATGACGAGGCACACACATTTTAAGTTCGat                                                         >  1:3341423/1‑69 (MQ=255)
        aCAATCAGATGGAATAAATGGCGCGATAACGCTCATTTTATGACGAGGCACACACATTTTAAGTTCGat                                                         >  1:3668893/1‑69 (MQ=255)
        aCAATCAGATGGAATAAATGGCGCGATAACGCTCATTTTATGACGAGGCACACACATTTTAAGTTCGat                                                         >  1:790612/1‑69 (MQ=255)
         cAATCAGATGGAATAAATGGCGCGATAACGCTCATTTTATGACGAGGCACACACATTTTAAGTTCGat                                                         <  1:3226689/68‑1 (MQ=255)
             cAGATGGAATAAATGGCGCGATAACGCTCATTTTATGACGAGGCACACACATTTTAAGTTCGATATTtc                                                    >  1:3370302/1‑69 (MQ=255)
              aGATGGAATAAATGGCGCGATAACGCTCATTTTATGACGAGGCACACACATTTTAAGTTCGATATTtct                                                   >  1:3062736/1‑69 (MQ=255)
              aGATGGAATAAATGGCGCGATAACGCTCATTTTATGACGAGGCACACACATTTTAAGTTCGATATTtct                                                   >  1:3186035/1‑69 (MQ=255)
              aGATGGAATAAATGGCGCGATAACGCTCATTTTATGACGAGGCACACACATTTTAAGTTCGATATTtct                                                   >  1:2604901/1‑69 (MQ=255)
                  ggAATAAATGGCGCGATAACGCTCATTTTATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGtt                                               >  1:2701849/1‑69 (MQ=255)
                        aaTGGCGCGATAACGCTCATTTTATGACGAGGCACACACATTTTAAGTTCGATATTTCTCGt                                                >  1:2673172/1‑62 (MQ=255)
                        aaTGGCGCGATAACGCTCATTTTATGACGAGGCACACACATTTTAAGTTCGATATTTCTCGt                                                >  1:2796391/1‑62 (MQ=255)
                        aaTGGCGCGATAACGCTCATTTTATGACGAGGCACACACATTTTAAGTTCGATATTTCTCGTTTTTGc                                          >  1:3058986/1‑68 (MQ=255)
                        aaTGGCGCGATAACGCTCATTTTATGACGAGGCACACACATTTTAAGTTCGATATTTCTCGTTTTTGCt                                         >  1:772040/1‑69 (MQ=255)
                        aaTGGCGCGATAACGCTCATTTTATGACGAGGCACACACATTTTAAGTTCGATATTTCTCGTTTTTGCt                                         >  1:1406800/1‑69 (MQ=255)
                            gcgcGATAACGCTCATTTTATGACGAGGCACACACATTTTAAGTTCGATATTTCTCGTTTTTGCTCGtt                                     <  1:2280088/69‑1 (MQ=255)
                            gcgcGATAACGCTCATTTTATGACGAGGCACACACATTTTAAGTTCGATATTTCTCGTTTTTGCTCGtt                                     <  1:3600686/69‑1 (MQ=255)
                            gcgcGATAACGCTCATTTTATGACGAGGCACACACATTTTAAGTTCGATATTTCTCGTTTTTGCTCGtt                                     <  1:1393633/69‑1 (MQ=255)
                                   aaCGCTCATTTTATGACGAGGCACACACATTTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATa                              >  1:602986/1‑69 (MQ=255)
                                    aCGCTCATTTTATGACGATGCACACACATTTTAAGTTCGatat                                                       >  1:1598439/1‑43 (MQ=255)
                                    aCGCTCATTTTATGACGAGGCACAGACATTTTAAGTTCGatat                                                       >  1:281889/1‑43 (MQ=255)
                                    aCGCTCATTTTATGACGAGGCACACACATTTTAAGTTCGatat                                                       >  1:445992/1‑43 (MQ=255)
                                    aCGCTCATTTTATGACGAGGCACACACATTTTAAGTTCGatat                                                       >  1:2839942/1‑43 (MQ=255)
                                       cTCATTTTATGACGAGGCACACACATTTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGtt                          <  1:336457/69‑1 (MQ=255)
                                       cTCATTTTATGACGAGGCACACACATTTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGtt                          <  1:2298242/69‑1 (MQ=255)
                                       cTCATTTTATGACGAGGCACACACATTTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGtt                          <  1:551109/69‑1 (MQ=255)
                                       cTCATTTTATGACGAGGCACACACATTTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGtt                          <  1:1113937/69‑1 (MQ=255)
                                       cTCATTTTATGACGAGGCACACACATTTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGtt                          <  1:837690/69‑1 (MQ=255)
                                          aTTTTATGACGAGGCACACACATTTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTAc                       >  1:787512/1‑69 (MQ=255)
                                          aTTTTATGACGAGGCACACACATTTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTAc                       >  1:1647225/1‑69 (MQ=255)
                                            tttATGACGAGGCACACACATTTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTAc                       <  1:1328355/67‑1 (MQ=255)
                                            tttATGACGAGGCACACACATTTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTAc                       <  1:621449/67‑1 (MQ=255)
                                            tttATGACGAGGCACACACATTTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTAc                       <  1:3450109/67‑1 (MQ=255)
                                            tttATGACGAGGCACACACATTTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTAc                       <  1:2570101/67‑1 (MQ=255)
                                            tttATGACGAGGCACACACATTTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTACAg                     <  1:1442832/69‑1 (MQ=255)
                                            tttATGACGAGGCACACACATTTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTACAg                     <  1:2953888/69‑1 (MQ=255)
                                            tttATGACGAGGCACACACATTTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTACAg                     <  1:75574/69‑1 (MQ=255)
                                            tttATGACGAGGCACACACATTTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTACAg                     <  1:3213714/69‑1 (MQ=255)
                                            tttATGACGAGGCACACACATTTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTACAg                     <  1:2808716/69‑1 (MQ=255)
                                            tttATGACGAGGCACACACATTTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTACAg                     <  1:2050964/69‑1 (MQ=255)
                                            tttATGACGAGGCACACACATTTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTACAg                     <  1:2420614/69‑1 (MQ=255)
                                            tttATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCt                                         <  1:3134858/49‑1 (MQ=255)
                                            tttATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCt                                         <  1:2863955/49‑1 (MQ=255)
                                            tttATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCt                                         <  1:197832/49‑1 (MQ=255)
                                            tttATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCt                                         <  1:2096193/49‑1 (MQ=255)
                                            tttATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCt                                         >  1:887556/1‑49 (MQ=255)
                                            tttATGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCt                                         >  1:2232101/1‑49 (MQ=255)
                                             ttATGACGAGGCACACACATTTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAAc                                  <  1:2230443/55‑1 (MQ=255)
                                             ttATGACGAGGCACACACATTTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAAc                                  <  1:455742/55‑1 (MQ=255)
                                             ttATGACGAGGCACACACATTTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTACAg                     >  1:545765/1‑68 (MQ=255)
                                                tGACGAGGCACACACATCTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTACAGCAt                  <  1:1763485/68‑1 (MQ=255)
                                                          cacacaTTTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTACAGCATGCCTACAAGCa       >  1:335273/1‑69 (MQ=255)
                                                          cacacaTTTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTACAGCATGCCTACAAGCa       >  1:905931/1‑69 (MQ=255)
                                                          cacacaTTTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTACAGCATGCCTACAAGCa       >  1:3529270/1‑69 (MQ=255)
                                                          cacacaTCTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTACAGCATGCCTACAAGCa       >  1:2580779/1‑69 (MQ=255)
                                                            cacaTTTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTa                        <  1:3416262/50‑1 (MQ=255)
                                                            cacaTTTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTa                        <  1:1714119/50‑1 (MQ=255)
                                                            cacaTTTTAAGTTCGATATTCCTCGTTTTTGCTCGTTAACGATAAGTTTa                        <  1:1190664/50‑1 (MQ=255)
                                                             acaTTTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGttt                         <  1:3666913/48‑1 (MQ=255)
                                                             acaTTTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGttt                         <  1:2346671/48‑1 (MQ=255)
                                                             acaTTTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTACAGCATGCCTACAAGCATCg    <  1:1319647/69‑1 (MQ=255)
                                                              caTTTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTACAGCATGCCTACAAGCATCg    <  1:1284697/68‑1 (MQ=255)
                                                               aTTTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTACAGCATGc                <  1:865297/55‑1 (MQ=255)
                                                               aTTTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTACAGCATGCCTACAAGCATCGTg  <  1:1449128/69‑1 (MQ=255)
                                                               aTTTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTACAGCATGCCTACAAGCATCGTg  <  1:2885372/69‑1 (MQ=255)
                                                               aTTTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTACAGCATGCCTACAAGCATCGTg  >  1:1018766/1‑69 (MQ=255)
                                                               aTTTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTACAGCATGCCTACAAGCATCGTg  <  1:95575/69‑1 (MQ=255)
                                                               aTTTTAAGTTCGATATTTCTAGTTTTTGCTCGTTAACGATAAGTTTACAGCATGCCTACAAGCATCGTg  >  1:1817810/1‑69 (MQ=255)
                                                                 |                                                                  
CATCATGTACAATCAGATGGAATAAATGGCGCGATAACGCTCATTTTATGACGAGGCACACACATTTTAAGTTCGATATTTCTCGTTTTTGCTCGTTAACGATAAGTTTACAGCATGCCTACAAGCATCGTG  >  W3110S.gb/3518406‑3518537

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A