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
A6 F21 I0 R2 370 72.1 3738297 91.5% 3420541 62.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,804,090 G→A 27.1% G52G (GGG→GGA)  mprA → DNA‑binding transcriptional regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,804,0900GA27.1% 178.0 / 76.9 107G52G (GGG→GGA) mprADNA‑binding transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base G (38/40);  new base A (15/14);  total (53/54)
Fisher's exact test for biased strand distribution p-value = 8.30e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.41e-01

Only 100 of 110 total aligned reads displayed.

ACTCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGCCTTCT  >  minE/1804022‑1804159
                                                                    |                                                                     
aCTCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGa                                                                      <  1:3591076/70‑1 (MQ=255)
 cTCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGAt                                                                     >  1:3276313/1‑70 (MQ=255)
 cTCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGAt                                                                     >  1:927652/1‑70 (MQ=255)
  tCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAAtt                                                                    >  1:2631967/1‑70 (MQ=255)
    gTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTa                                                                   <  1:483911/69‑1 (MQ=255)
    gTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAAc                                                                 <  1:3326595/71‑1 (MQ=255)
    gTCTTTGCATGAACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAAc                                                                 >  1:1136639/1‑71 (MQ=255)
       tttGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGAtt                                                                    <  1:2286913/65‑1 (MQ=255)
       tttGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAAc                                                                 >  1:2610204/1‑68 (MQ=255)
       tttGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAAc                                                                 >  1:3006976/1‑68 (MQ=255)
       tttGCATGCACATGCAAACCAATCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAAc                                                                 >  1:1068315/1‑68 (MQ=255)
         tgcatgcaCATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACga                                                               >  1:1404246/1‑68 (MQ=255)
               cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttgtt                                                      <  1:1852676/71‑1 (MQ=255)
               cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttgtt                                                      >  1:462909/1‑71 (MQ=255)
               cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttgt                                                       <  1:2211289/70‑1 (MQ=255)
               cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttgt                                                       <  1:1767349/70‑1 (MQ=255)
                acatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGAc                                                            >  1:443950/1‑64 (MQ=255)
                acatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgtt                                                         <  1:2659722/67‑1 (MQ=255)
                acatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGttt                                                     <  1:2241385/71‑1 (MQ=255)
                acatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGgtt                                                     <  1:254323/71‑1 (MQ=255)
                acatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                      >  1:1546220/1‑70 (MQ=255)
                 catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTa                                                    <  1:51348/71‑1 (MQ=255)
                 catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTa                                                    <  1:68721/71‑1 (MQ=255)
                  atgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACg                                                                <  1:3640033/58‑1 (MQ=255)
                  atgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTAt                                                   <  1:3539313/71‑1 (MQ=255)
                    gcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATgg                                                 >  1:1991566/1‑71 (MQ=255)
                    gcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATgg                                                 >  1:169927/1‑71 (MQ=255)
                    gcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATgg                                                 >  1:1960526/1‑71 (MQ=255)
                    gcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAAtt                                                                    >  1:1313133/1‑52 (MQ=255)
                    gcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATgg                                                 >  1:3632441/1‑71 (MQ=255)
                      aaaGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCg                                               >  1:835773/1‑71 (MQ=255)
                       aagcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACgaga                                                             >  1:3008321/1‑56 (MQ=255)
                       aagcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACgaga                                                             >  1:1258244/1‑56 (MQ=255)
                       aagcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTa                                                                   <  1:1487343/50‑1 (MQ=255)
                       aagcaagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTa                                                                   <  1:3113493/50‑1 (MQ=255)
                          caagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGAtt                                                                    <  1:2487641/46‑1 (MQ=255)
                          caagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGAtt                                                                    <  1:3396318/46‑1 (MQ=255)
                           aagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACgaga                                                             >  1:3237499/1‑52 (MQ=255)
                           aagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACgaga                                                             >  1:637230/1‑52 (MQ=255)
                            agcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGAtt                                         <  1:2321422/71‑1 (MQ=255)
                               tgctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTaa                                                                  >  1:1096951/1‑43 (MQ=255)
                               tgctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTaa                                                                  >  1:2049095/1‑43 (MQ=255)
                               tgctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTaa                                                                  >  1:2042416/1‑43 (MQ=255)
                                 ctgGAGAACCGCAATAATATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTa                                                    <  1:2266813/55‑1 (MQ=255)
                                 ctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGc                                     >  1:563483/1‑70 (MQ=255)
                                 ctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACg                                      <  1:3338955/69‑1 (MQ=255)
                                 ctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACg                                      <  1:1035185/69‑1 (MQ=255)
                                 ctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACg                                      <  1:1849819/69‑1 (MQ=255)
                                 ctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGc                                     <  1:3428574/70‑1 (MQ=255)
                                 ctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGc                                     <  1:556864/70‑1 (MQ=255)
                                   ggAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                                   >  1:3268076/1‑70 (MQ=255)
                                    gagaACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGc                                     <  1:1389154/67‑1 (MQ=255)
                                    gagaACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTgg                                  <  1:2338380/70‑1 (MQ=255)
                                    gagaACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                                   <  1:383610/69‑1 (MQ=255)
                                    gagaACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTg                                   <  1:2241521/69‑1 (MQ=255)
                                     agaACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgt                                                          <  1:2613525/45‑1 (MQ=255)
                                     agaACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgt                                                          <  1:572072/45‑1 (MQ=255)
                                     agaACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTa                                                    >  1:2536212/1‑51 (MQ=255)
                                     agaACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTa                                                    >  1:3283970/1‑51 (MQ=255)
                                         ccGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGc                                     <  1:759236/62‑1 (MQ=255)
                                         ccGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCt                                    <  1:3490230/63‑1 (MQ=255)
                                         ccGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCt                                    <  1:3360868/63‑1 (MQ=255)
                                         ccGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCt                                    <  1:2736825/63‑1 (MQ=255)
                                         ccGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCt                                    <  1:2751882/63‑1 (MQ=255)
                                         ccGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACCTTGTTTATGGCGTTGATTACGCTGGAGtctc                            <  1:815862/71‑1 (MQ=255)
                                            cAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTg                                            <  1:1262720/52‑1 (MQ=255)
                                            cAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAg                          >  1:956780/1‑70 (MQ=255)
                                            cAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAg                          >  1:1132275/1‑70 (MQ=255)
                                            cAATAAAATGCTGAAGGCTCAGGGGATTAACCAGACGTTGTTTATGGCGTTGa                                           >  1:2293334/1‑53 (MQ=255)
                                            cAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAgg                         <  1:3202036/71‑1 (MQ=255)
                                            cAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAg                          >  1:747647/1‑70 (MQ=255)
                                            cAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAg                          >  1:808771/1‑70 (MQ=255)
                                             aaTAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAgg                         >  1:3441847/1‑70 (MQ=255)
                                               tAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaa                       >  1:104061/1‑70 (MQ=255)
                                               tAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGa                        >  1:717482/1‑69 (MQ=255)
                                                aaaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTa                                                    >  1:2026765/1‑40 (MQ=255)
                                                aaaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTa                                                    >  1:273558/1‑40 (MQ=255)
                                                 aaaTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGa                                 <  1:336996/58‑1 (MQ=255)
                                                 aaaTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGa                                 <  1:3388000/58‑1 (MQ=255)
                                                  aaTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGa                                 <  1:2724663/57‑1 (MQ=255)
                                                  aaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAAcc                   <  1:1130534/71‑1 (MQ=255)
                                                   aTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGc                                                >  1:2484312/1‑41 (MQ=255)
                                                   aTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGc                                                >  1:2067857/1‑41 (MQ=255)
                                                   aTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGc                                                >  1:2612690/1‑41 (MQ=255)
                                                   aTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGc                                                >  1:2768248/1‑41 (MQ=255)
                                                   aTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGc                                                >  1:3179388/1‑41 (MQ=255)
                                                   aTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACca                  <  1:2552107/71‑1 (MQ=255)
                                                   aTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACca                  <  1:46340/71‑1 (MQ=255)
                                                         aaGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTa             >  1:2408534/1‑70 (MQ=255)
                                                         aaGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTAt            >  1:159384/1‑71 (MQ=255)
                                                           ggCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCt                                    >  1:291801/1‑45 (MQ=255)
                                                           ggCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCt                                    >  1:1101950/1‑45 (MQ=255)
                                                            gCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCa         <  1:240282/71‑1 (MQ=255)
                                                             cTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAg        <  1:3684952/71‑1 (MQ=255)
                                                               cAGGGAATTAACGAGACGGTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAAcc                   >  1:1187668/1‑58 (MQ=255)
                                                                aGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTa             <  1:269794/63‑1 (MQ=255)
                                                                aGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGCCt     <  1:1517982/71‑1 (MQ=255)
                                                                  gggATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACca                  >  1:1271773/1‑56 (MQ=255)
                                                                   ggATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGCCTTCt  <  1:437064/71‑1 (MQ=255)
                                                                   ggATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGCCTTCt  <  1:1223587/71‑1 (MQ=255)
                                                                    |                                                                     
ACTCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAGCCTTCT  >  minE/1804022‑1804159

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