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 F28 I3 R1 375 42.1 2927644 71.4% 2090337 57.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA W3110S.gb 2,809,581 G→A G52G (GGG→GGA)  mprA → DNA‑binding transcriptional regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb2,809,5810GA99.0% 1281.5 / ‑1.1 380G52G (GGG→GGA) mprADNA‑binding transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base G (0/4);  new base A (198/178);  total (198/182)
Fisher's exact test for biased strand distribution p-value = 5.17e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.86e-01

Only 100 of 380 total aligned reads displayed.

GCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACA  >  W3110S.gb/2809527‑2809636
                                                      |                                                       
gcacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTa                                                     >  1:405702/1‑59 (MQ=255)
gcacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTa                                                     >  1:269760/1‑59 (MQ=255)
gcacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTa                                                     >  1:165533/1‑59 (MQ=255)
gcacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTa                                                     >  1:2353940/1‑59 (MQ=255)
gcacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTa                                                     >  1:1909308/1‑59 (MQ=255)
gcacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTa                                                     >  1:2369328/1‑59 (MQ=255)
gcacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTa                                                     >  1:592865/1‑59 (MQ=255)
  acatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACgag                                                >  1:2326785/1‑62 (MQ=255)
  acatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACgag                                                >  1:1849792/1‑62 (MQ=255)
  acatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACgag                                                >  1:1172479/1‑62 (MQ=255)
   catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACgaga                                               <  1:1583940/62‑1 (MQ=255)
   catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACgaga                                               <  1:1519133/62‑1 (MQ=255)
   catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACgaga                                               <  1:2031538/62‑1 (MQ=255)
   catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACgaga                                               <  1:676837/62‑1 (MQ=255)
   catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACgaga                                               <  1:1746016/62‑1 (MQ=255)
   catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACgaga                                               <  1:1877834/62‑1 (MQ=255)
   catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACgaga                                               <  1:1790255/62‑1 (MQ=255)
   catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACgaga                                               <  1:628828/62‑1 (MQ=255)
   catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACgaga                                               <  1:2388471/62‑1 (MQ=255)
   catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACgaga                                               <  1:2435717/62‑1 (MQ=255)
   catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACgaga                                               <  1:2468050/62‑1 (MQ=255)
   catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACgaga                                               <  1:2792640/62‑1 (MQ=255)
   catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACgaga                                               <  1:2743321/62‑1 (MQ=255)
   catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACgaga                                               <  1:1268143/62‑1 (MQ=255)
   catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACgaga                                               <  1:2550369/62‑1 (MQ=255)
   catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACgaga                                               <  1:1133664/62‑1 (MQ=255)
   catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACgaga                                               <  1:971235/62‑1 (MQ=255)
   catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACgaga                                               <  1:1097197/62‑1 (MQ=255)
   catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACgaga                                               <  1:1013124/62‑1 (MQ=255)
   catgcaAAGCAAGCTGCGGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACgaga                                               <  1:1932770/62‑1 (MQ=255)
    atgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACgaga                                               <  1:1891286/61‑1 (MQ=255)
        aaaGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttg                                          >  1:1155207/1‑62 (MQ=255)
        aaaGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttg                                          >  1:1345720/1‑62 (MQ=255)
        aaaGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttg                                          >  1:1330092/1‑62 (MQ=255)
        aaaGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttg                                          >  1:875057/1‑62 (MQ=255)
        aaaGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttg                                          >  1:33783/1‑62 (MQ=255)
        aaaGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttg                                          >  1:467320/1‑62 (MQ=255)
        aaaGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttg                                          >  1:496993/1‑62 (MQ=255)
        aaaGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttg                                          >  1:2114712/1‑62 (MQ=255)
        aaaGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttg                                          >  1:798405/1‑62 (MQ=255)
        aaaGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttg                                          >  1:1999060/1‑62 (MQ=255)
        aaaGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttg                                          >  1:1634342/1‑62 (MQ=255)
        aaaGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttg                                          >  1:1601218/1‑62 (MQ=255)
            caagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgt                                            <  1:2229947/56‑1 (MQ=255)
            caagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgt                                            <  1:1757072/56‑1 (MQ=255)
            caagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgt                                            <  1:1363597/56‑1 (MQ=255)
            caagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgt                                            <  1:946356/56‑1 (MQ=255)
            caagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgt                                            <  1:652420/56‑1 (MQ=255)
            caagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgt                                            <  1:2919230/56‑1 (MQ=255)
            caagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgt                                            <  1:1075211/56‑1 (MQ=255)
            caagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgt                                            <  1:815183/56‑1 (MQ=255)
            caagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgt                                            <  1:1982872/56‑1 (MQ=255)
            caagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgt                                            <  1:1942264/56‑1 (MQ=255)
            caagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgt                                            <  1:54430/56‑1 (MQ=255)
            caagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgt                                            <  1:2605571/56‑1 (MQ=255)
            caagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTa                                      <  1:2701769/62‑1 (MQ=255)
             aagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACgaga                                               <  1:1555351/52‑1 (MQ=255)
             aagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgt                                            <  1:76334/55‑1 (MQ=255)
              agcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTa                                                     >  1:2680342/1‑45 (MQ=255)
              agcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                        >  1:2405879/1‑58 (MQ=255)
              agcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                        >  1:1394403/1‑58 (MQ=255)
              agcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                        >  1:916946/1‑58 (MQ=255)
              agcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                        >  1:1303991/1‑58 (MQ=255)
              agcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                        >  1:424467/1‑58 (MQ=255)
              agcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                        >  1:525134/1‑58 (MQ=255)
              agcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                        >  1:2560965/1‑58 (MQ=255)
              agcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                        >  1:1969629/1‑58 (MQ=255)
              agcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                        >  1:1701132/1‑58 (MQ=255)
              agcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATg                                    >  1:2871483/1‑62 (MQ=255)
              agcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATg                                    >  1:1044411/1‑62 (MQ=255)
              agcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATg                                    >  1:1548159/1‑62 (MQ=255)
              agcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATg                                    >  1:2508405/1‑62 (MQ=255)
              agcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATg                                    >  1:2195538/1‑62 (MQ=255)
              agcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATg                                    >  1:2239556/1‑62 (MQ=255)
              agcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATg                                    >  1:2290997/1‑62 (MQ=255)
              agcTGCTGGAGAACCGCAATAAAATGCTGAAGGATCAGGGAATTAACGAGACgttgtt                                        >  1:2143312/1‑58 (MQ=255)
              agcTCCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACgaga                                               >  1:2159921/1‑51 (MQ=255)
                   ctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACgag                                                >  1:2524058/1‑45 (MQ=255)
                   ctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGtt                               >  1:1425699/1‑62 (MQ=255)
                   ctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGtt                               >  1:2635583/1‑62 (MQ=255)
                       agaACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACgaga                                               <  1:716312/42‑1 (MQ=255)
                       agaACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGAtt                           >  1:1122080/1‑62 (MQ=255)
                           ccGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGc                       <  1:2819336/62‑1 (MQ=255)
                           ccGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGc                       <  1:252045/62‑1 (MQ=255)
                           ccGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGc                       <  1:1451795/62‑1 (MQ=255)
                           ccGCAATAAAATGCTGAAGGCTCAGGCAATTAACGAGACGTTGTTTATGGCGTTGATTACGc                       <  1:84357/62‑1 (MQ=255)
                            cGCAATAAAATGCTGAAGGCTCAGGGATTTAACGAGACGTTGTTTATGGCGTTGATTACGc                       <  1:1332845/61‑1 (MQ=255)
                                           aaGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaaaa       <  1:19533/62‑1 (MQ=255)
                                             ggCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaaaa       <  1:154087/60‑1 (MQ=255)
                                             ggCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaaaa       <  1:1482871/60‑1 (MQ=255)
                                             ggCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaaaa       <  1:2040122/60‑1 (MQ=255)
                                             ggCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaaaa       <  1:2078669/60‑1 (MQ=255)
                                             ggCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaaaa       <  1:2481673/60‑1 (MQ=255)
                                             ggCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaaaa       <  1:2854054/60‑1 (MQ=255)
                                              gCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaaaa       <  1:700545/59‑1 (MQ=255)
                                               cTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACcac   >  1:1565203/1‑62 (MQ=255)
                                               cTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACcac   >  1:1647077/1‑62 (MQ=255)
                                               cTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACcac   >  1:1719806/1‑62 (MQ=255)
                                               cTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACcac   >  1:2253614/1‑62 (MQ=255)
                                               cTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACcac   >  1:984157/1‑62 (MQ=255)
                                                      |                                                       
GCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACA  >  W3110S.gb/2809527‑2809636

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A