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
A5 F21 I0 R2 316 65.6 5147759 97.4% 5013917 60.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 4,281,027 T→C 30.8% intergenic (‑52/‑34) soxS ← / → soxR DNA‑binding transcriptional dual regulator/DNA‑binding transcriptional dual regulator, Fe‑S center for redox‑sensing

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb4,281,0270TC30.8% 66.1 / 44.0 52intergenic (‑52/‑34)soxS/soxRDNA‑binding transcriptional dual regulator/DNA‑binding transcriptional dual regulator, Fe‑S center for redox‑sensing
Reads supporting (aligned to +/- strand):  ref base T (12/24);  new base C (8/8);  total (20/32)
Fisher's exact test for biased strand distribution p-value = 3.56e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.83e-01

ATTTTCTGATGGGACATAAATCTGCCTCTTTTCAGTGTTCAGTTCGTTAATTCATCTGTTGGGGAGTATAATTCCTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCT  >  W3110S.gb/4280959‑4281095
                                                                    |                                                                    
atTTTCTGATGGGACATAAATCTGCCTCTTTTCAGTGTTCAGTTCGTTAATTCATCTGTTGGGGAGtata                                                                     >  1:292084/1‑70 (MQ=255)
atTTTCTGATGGGACATAAATCTGCCTCTTTTCAGTGTTCAGTTCGTTAATTCATCTGTTGGGGAGtata                                                                     <  1:4752079/70‑1 (MQ=255)
atTTTCTGATGGGACATAAATCTGCCTCTTTTCAGTGTTCAGTTCGTTAATTCATCTGTTGGGGAGTATaa                                                                    >  1:4556220/1‑71 (MQ=255)
 ttttCTGATGGGACATAAATCTGCCTCTTTTCAGTGTTCAGTTCGTTAATTCATCTGTTGGGGAGTATAAt                                                                   <  1:4160587/71‑1 (MQ=255)
           ggACATAAATCTGCCTCTTTTCAGTGTTCAGTTCGTTAATTCATCTGTTGGGGAGTATAATTCCTCAAGtt                                                         <  1:2352111/71‑1 (MQ=255)
           ggACATAAATCTGCCTCTTTTCAGTGTTCAGTTCGTTAATTCATCTGTTGGGGAGTATAATTCCTCAAGtt                                                         <  1:1821442/71‑1 (MQ=255)
              cATAAATCTGCCTCTTTTCAGTGTTCAGTTCGTTAATTCATCTGTTGGGGAGTACAATTCCTCAAGTTAAc                                                      <  1:3733993/71‑1 (MQ=255)
               aTAAATCTGCCTCTTTTCAGTGTTCAGTTCGTTAATTCATCTGTTGGGGAGTATAATTCCTCa                                                             <  1:4174743/63‑1 (MQ=255)
                tAAATCTGCCTCTTTTCAGTGTTCAGTTCGTTAATTCATCTGTTGGGGAGTACAAt                                                                   <  1:643332/56‑1 (MQ=255)
                  aaTCTGCCTCTTTTCAGTGTTCAGTTCGTTAATTCATCTGTTGTGGAGTACAATTCCTCAAGTTAACtt                                                    >  1:1753229/1‑69 (MQ=255)
                   aTCTGCCTCTTTTCAGTGTTCAGTTCGTTAATTCATCTGTTGGGGAGTATAATTCCTCAAGTTAACTTGAg                                                 >  1:2649464/1‑71 (MQ=255)
                   aTCTGCCTCTTTTCAGTGTTCAGTTCGTTAATTCATCTGTTGGGGAGTATAATTCCTCAAGTTAACTTGAg                                                 >  1:2535827/1‑71 (MQ=255)
                   aTCTGCCTCTTTTCAGTGTTCAGTTCGTTAATTCATCTGTTGGGGAGTATAATTCCTCAAGTTAACTTGAg                                                 >  1:4316336/1‑71 (MQ=255)
                    tCTGCCTCTTTTCAGTGTTCAGTTCGTTAATTCATCTGTTGGGGAGTATAATTCCTCAAGTTAACTTg                                                   <  1:1584804/68‑1 (MQ=255)
                        ccTCTTTTCAGTGTTCAGTTCGTTAATTCATCTGTTGGGGAGTATAATTCCTCAAGTTAACTTGAGGTa                                              <  1:866852/69‑1 (MQ=255)
                        ccTCTTTTCAGTGTTCAGTTCGTTAATTCATCTGTTGGGGAGTATAATTCCTCAAGTTAACTTGAGGTa                                              <  1:197042/69‑1 (MQ=255)
                        ccTCTTTTCAGTGTTCAGTTCGTTAATTCATCTGTTGGGGAGTATAATTCCTCAAGTTAACTTGAGGTa                                              <  1:4481059/69‑1 (MQ=255)
                        ccTCTTTTCAGTGTTCAGTTCGTTAATTCATCTGTTGGGGAGTACAATTCCTCAAGTTAACTTGAGGTa                                              >  1:1675134/1‑69 (MQ=255)
                        ccTCTTTTCAGTGTTCAGTTCGTTAATTCATCTGTTGGGGAGTACAATTCCTCAAGTTAACTTGAGGTa                                              >  1:4629623/1‑69 (MQ=255)
                         ctctTTTCAGTGTTCAGTTCGTTAATTCATCTGTTGGGGAGTATAATTCCTCa                                                             <  1:3350615/53‑1 (MQ=255)
                          tctTTTCAGTGTTCAGTTCGTTAATTCATCTGTTGGGGAGTACAATTCCTCAAGTTAACTTg                                                   <  1:4156611/62‑1 (MQ=255)
                           ctTTTCAGTGTTCAGTTCGTTAATTCATCTGTTGGGGAGTACAATTCCTCAAGTTAACTTGAGGTAAAGc                                          >  1:1610343/1‑70 (MQ=255)
                            ttttCAGTGTTCAGTTCGTTAATTCATCTGTTGGGGAGTATAATTCCTCAAGTTAACTTGAgg                                                <  1:3823460/63‑1 (MQ=255)
                            ttttCAGTGTTCAGTTCGTTAATTCATCTGTTGGGGAGTACAAt                                                                   >  1:4167298/1‑44 (MQ=255)
                            ttttCAGTGTTCAGTTCGTTAATTCATCTGTTGGGGAGTACAAt                                                                   >  1:4124069/1‑44 (MQ=255)
                            ttttCAGTGTTCAGTTCGTTAATTCATCTGTTGGGGAGTACAAt                                                                   >  1:90833/1‑44 (MQ=255)
                            ttttCAGTGTTCAGTTCGTTAATTCATCTGTTGGGGAGTACAATTCCTCAAGTTAACTTGAGGTAAAGCGa                                        >  1:4708218/1‑71 (MQ=255)
                              ttCAGTGTTCAGTTCGTTAATTCATCTGTTGGGGAGTATAATTCCTCAAGTTAACTTGAGGTa                                              >  1:594352/1‑63 (MQ=255)
                              ttCAGTGTTCAGTTCGTTAATTCATCTGTTGGGGAGTATAATTCCTCAAGTTAACATGAGGTa                                              >  1:977588/1‑63 (MQ=255)
                               tCAGTGTTCAGTTCGTTAATTCATCTGTTGGGGAGTATAATTCCTCAAGTTAACTTGAgg                                                <  1:2517230/60‑1 (MQ=255)
                                 aGTGTTCAGTTCGTTAATTCATCTGTTGGGGAGTATAATTCCTCAAGTTAACTTGAGGTAAAGCGATTTa                                    <  1:4179065/70‑1 (MQ=255)
                                     ttCAGTTCGTTAATTCATCTGTTGGGGAGTATAATTCCTCa                                                             <  1:4381047/41‑1 (MQ=255)
                                     ttCAGTTCGTTAATTCATCTGTTGGGGAGTACAATTCCTCAAGTTa                                                        <  1:615651/46‑1 (MQ=255)
                                     ttCAGTTCGTTAATTCATCTGTTGGGGAGTACAATTCCTCAAGTTAACTTGAGGTAAAGc                                          <  1:3752699/60‑1 (MQ=255)
                                     ttCAGTTCGTTAATTCATCTGTTGGGGAGTACAATTCCTCAAGTTAACTTGAGGTAAAGc                                          <  1:1147192/60‑1 (MQ=255)
                                       cAGTTCGTTAATTCATCTGTTGGGGAGTATAATTCCTCAAg                                                           >  1:1112390/1‑41 (MQ=255)
                                       cAGTTCGTTAATTCATCTGTTGGGGAGTATAATTCCTCAAGTTAACTTGAGGTa                                              <  1:489900/54‑1 (MQ=255)
                                        aGTTCGTTAATTCATCTGTTGGGGAGTACAATTCCTCAAGTTAACTTGAGGTAAAGCGATTTATGGaaaa                             <  1:1749138/70‑1 (MQ=255)
                                         gTTCGTTAATTCATCTGTTGGGGAGTATAATTCTTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGa                           <  1:910142/71‑1 (MQ=255)
                                          ttCGTTAATTCATCTGTTGGGGAGTATAATTCCTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGaa                          <  1:1131565/71‑1 (MQ=255)
                                            cGTTAATTCATCTGTTGGGGAGTATAATTCCTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAAt                        >  1:1685971/1‑71 (MQ=255)
                                             gTTAATTCATCTGTTGGGGAGTATAATTCCTCAAGTTaa                                                       <  1:4920747/39‑1 (MQ=255)
                                             gTTAATTCATCTGTTGGGGAGTATAATTCCTCAAGTTAACTTg                                                   <  1:111385/43‑1 (MQ=255)
                                             gTTAATTCATCTGTTGGGGAGTATAATTCCTCAAGTTAACTTg                                                   <  1:1684204/43‑1 (MQ=255)
                                               tAATTCATCTGTTGGGGAGTATAATTCCTCAAGTTAAc                                                      >  1:1772208/1‑38 (MQ=255)
                                               tAATTCATCTGTTGGGGAGTATAATTCCTCAAGTTAACTTGAg                                                 >  1:213421/1‑43 (MQ=255)
                                                aaTTCATCTGTTGGGGAGTACAATTCCTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGa                           <  1:1298860/64‑1 (MQ=255)
                                                      tCTGTTGGGGAGTATAATTCCTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGa                           <  1:625285/58‑1 (MQ=255)
                                                      tCTGTTGGGGAGTATAATTCCTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCAt              >  1:3646550/1‑71 (MQ=255)
                                                          ttGGGGAGTATAATTCCTCAAGTTAACTTGAGGTAAAGCGAt                                       >  1:2969375/1‑42 (MQ=255)
                                                          ttGGGGAGTATAATTCCTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTa            <  1:2828240/69‑1 (MQ=255)
                                                          ttGGGGAGTATAATTCCTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTa            <  1:2569319/69‑1 (MQ=255)
                                                          ttGGGGAGTATAATTCCTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTa            <  1:891075/69‑1 (MQ=255)
                                                            ggggAGTATAATTCCTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAg         <  1:4114449/70‑1 (MQ=255)
                                                                  tataATTCCTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCgctgct  <  1:2009641/71‑1 (MQ=255)
                                                                  tataATTCCTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCgctgc   >  1:3955633/1‑70 (MQ=255)
                                                                    taATTCCTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGaaa                         >  1:2055101/1‑46 (MQ=255)
                                                                    taATTCCTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGaaa                         >  1:1830851/1‑46 (MQ=255)
                                                                    taATTCCTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGa                           <  1:2952998/44‑1 (MQ=255)
                                                                    taATTCCTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGa                           <  1:3639271/44‑1 (MQ=255)
                                                                    taATTCCTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAAt                        <  1:2155883/47‑1 (MQ=255)
                                                                    |                                                                    
ATTTTCTGATGGGACATAAATCTGCCTCTTTTCAGTGTTCAGTTCGTTAATTCATCTGTTGGGGAGTATAATTCCTCAAGTTAACTTGAGGTAAAGCGATTTATGGAAAAGAAATTACCCCGCATTAAAGCGCTGCT  >  W3110S.gb/4280959‑4281095

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