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
A3 F21 I0 R1 61 33.6 2680365 96.0% 2573150 61.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 2,809,581 G→A 45.7% 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.gb2,809,5810GA45.7% 25.9 / 112.5 81G52G (GGG→GGA) mprADNA‑binding transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base G (15/29);  new base A (19/18);  total (34/47)
Fisher's exact test for biased strand distribution p-value = 1.75e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.74e-01

CGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGCC  >  W3110S.gb/2809516‑2809646
                                                                 |                                                                 
cGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTaa                                                              >  1:195964/1‑71 (MQ=255)
 gTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAAc                                                             <  1:1308917/71‑1 (MQ=255)
  tCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAAc                                                             >  1:1246402/1‑70 (MQ=255)
    tttGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAAc                                                             >  1:1342057/1‑68 (MQ=255)
    tttGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAAc                                                             >  1:451209/1‑68 (MQ=255)
    tttGCATGCACATGCAAAGCAAGCTGCTGGAGAACAGCAATAAAATGCTGAAGGCTCAGGGGATTAAc                                                             >  1:1918623/1‑68 (MQ=255)
    tttGCATGCACATGCAAAGCAAGCTGATGGAGAACAGCAATAAAATGCTGAAGGCTCAGGGGATTAAc                                                             >  1:2429989/1‑68 (MQ=255)
          tgcacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACga                                                           <  1:682256/64‑1 (MQ=255)
            cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACgaga                                                         >  1:1492823/1‑64 (MQ=255)
            cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                  <  1:524473/71‑1 (MQ=255)
            cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                  <  1:1613218/71‑1 (MQ=255)
              catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTa                                                <  1:1062952/71‑1 (MQ=255)
              catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTa                                                <  1:1981848/71‑1 (MQ=255)
              catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTa                                                <  1:321470/71‑1 (MQ=255)
              catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTa                                                <  1:659537/71‑1 (MQ=255)
                tgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACga                                                           >  1:952064/1‑58 (MQ=255)
                tgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATg                                              >  1:570219/1‑71 (MQ=255)
                tgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATg                                              >  1:947211/1‑71 (MQ=255)
                tgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATg                                              >  1:936728/1‑71 (MQ=255)
                 gcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATgg                                             >  1:800757/1‑71 (MQ=255)
                  caAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTa                                                >  1:1848753/1‑67 (MQ=255)
                  caAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATgg                                             >  1:2100722/1‑70 (MQ=255)
                  caAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGc                                            >  1:535427/1‑71 (MQ=255)
                      gcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGtt                                         >  1:1583985/1‑70 (MQ=255)
                      gcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGtt                                         >  1:1836113/1‑70 (MQ=255)
                      gcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTg                                        <  1:2450063/71‑1 (MQ=255)
                       caagcTGCTGGAGAACCTCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTa                                                >  1:1620767/1‑62 (MQ=255)
                       caagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTa                                                >  1:818919/1‑62 (MQ=255)
                       caagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTa                                                >  1:1086872/1‑62 (MQ=255)
                       caagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTa                                                >  1:1341483/1‑62 (MQ=255)
                       caagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTg                                        <  1:939344/70‑1 (MQ=255)
                        aagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGAt                                      <  1:1797859/71‑1 (MQ=255)
                        aagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGAt                                      <  1:1464407/71‑1 (MQ=255)
                        aagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGAt                                      <  1:2048479/71‑1 (MQ=255)
                        aagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGAt                                      <  1:1284607/71‑1 (MQ=255)
                        aagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGAt                                      <  1:532100/71‑1 (MQ=255)
                        aagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGAt                                      <  1:1090204/71‑1 (MQ=255)
                        aagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGAt                                      <  1:1875596/71‑1 (MQ=255)
                        aagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGAt                                      <  1:1844124/71‑1 (MQ=255)
                         agcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                  <  1:2654894/58‑1 (MQ=255)
                          gctgctGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGa                                       >  1:27766/1‑68 (MQ=255)
                            tgctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACg                                  >  1:2032324/1‑71 (MQ=255)
                               tgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACga                                                           <  1:928600/43‑1 (MQ=255)
                               tgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACga                                                           <  1:2133673/43‑1 (MQ=255)
                               tgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAAc                                                             <  1:2601342/41‑1 (MQ=255)
                               tgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAAc                                                             <  1:992616/41‑1 (MQ=255)
                               tgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACga                                                           <  1:2454769/43‑1 (MQ=255)
                                 gagaACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTgg                              <  1:2531950/70‑1 (MQ=255)
                                 gagaACAGCAATAAAATGCTGAAGGCTCAGGGAATTAAAgaga                                                         >  1:346524/1‑43 (MQ=37)
                                    aaCCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGtc                          <  1:1250901/71‑1 (MQ=255)
                                     aCCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGtct                         <  1:1848128/71‑1 (MQ=255)
                                     aCCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGtc                          <  1:1709543/70‑1 (MQ=255)
                                      ccGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGtctc                        <  1:1641118/71‑1 (MQ=255)
                                      cagCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCt                                >  1:63187/3‑63 (MQ=255)
                                       cGCAATAAAATGCTGAATGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGAt                                      <  1:2611378/56‑1 (MQ=255)
                                       cGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTa                                    >  1:1095702/1‑58 (MQ=255)
                                         cAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAg                      >  1:1573357/1‑70 (MQ=255)
                                           aTAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGc                                            <  1:1230430/46‑1 (MQ=255)
                                           aTAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaa                   <  1:1048348/71‑1 (MQ=255)
                                           aTAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaa                   <  1:1007365/71‑1 (MQ=255)
                                           aTAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaa                   <  1:2387754/71‑1 (MQ=255)
                                            tAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGAt                                      <  1:1069704/51‑1 (MQ=255)
                                              aaaTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaa                   <  1:2066698/68‑1 (MQ=255)
                                              aaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAAc                >  1:172689/1‑71 (MQ=255)
                                              aaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAAc                >  1:1779418/1‑71 (MQ=255)
                                              aaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAAc                >  1:1793426/1‑71 (MQ=255)
                                                aTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACca              <  1:1386411/71‑1 (MQ=255)
                                                aTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACca              <  1:1450471/71‑1 (MQ=255)
                                                   cTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAg           >  1:848267/1‑71 (MQ=255)
                                                   cTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAg           <  1:2046426/71‑1 (MQ=255)
                                                   cTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAg           >  1:2002503/1‑71 (MQ=255)
                                                   cTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAg           <  1:2335814/71‑1 (MQ=255)
                                                     gAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGAt                                      <  1:1349106/42‑1 (MQ=255)
                                                      aaGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTa         <  1:255813/70‑1 (MQ=255)
                                                      aaGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTa         <  1:1410634/70‑1 (MQ=255)
                                                      aaGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTa         <  1:245883/70‑1 (MQ=255)
                                                      aaGGCTCAGGGAATTAACGAGAAGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTa         <  1:539535/70‑1 (MQ=255)
                                                           tCAGGGGATTAACGAGACTTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGc   >  1:56959/1‑71 (MQ=255)
                                                           tCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAg           >  1:748260/1‑63 (MQ=255)
                                                             aGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGcc  <  1:444092/70‑1 (MQ=255)
                                                             aGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGcc  <  1:1381285/70‑1 (MQ=255)
                                                                 |                                                                 
CGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGCC  >  W3110S.gb/2809516‑2809646

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