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
A2 F1 I0 R1 4577 57.4 3436498 77.7% 2670158 63.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,804,090 G→A 90.1% G52G (GGG→GGA)  mprA → DNA‑binding transcriptional regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,804,0900GA90.1% 2008.5 / 118.9 998G52G (GGG→GGA) mprADNA‑binding transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base G (37/64);  new base A (333/563);  total (371/627)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.96e-01

Only 100 of 999 total aligned reads displayed.

TCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAG  >  minE/1804024‑1804153
                                                                  |                                                               
 cGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAAtt                                                              <  1:1955592/69‑1 (MQ=255)
  gTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTa                                                             >  1:1383284/1‑69 (MQ=255)
    cTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAAtt                                                              <  1:2575417/66‑1 (MQ=255)
     tttGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTa                                                             >  1:1847146/1‑66 (MQ=255)
     tttGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTa                                                             >  1:485161/1‑66 (MQ=255)
     tttGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTa                                                             >  1:547692/1‑66 (MQ=255)
     tttGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTa                                                             >  1:3275270/1‑66 (MQ=255)
     tttGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTa                                                             >  1:2951160/1‑66 (MQ=255)
     tttGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTa                                                             >  1:216275/1‑66 (MQ=255)
     tttGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTa                                                             >  1:82110/1‑66 (MQ=255)
     tttGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTa                                                             >  1:1015860/1‑66 (MQ=255)
     tttGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCT‑AGGGAATTAACga                                                         >  1:2655578/1‑69 (MQ=255)
           tgcacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAAc                                                           <  1:2014822/62‑1 (MQ=255)
           tgcacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAAc                                                           <  1:1533294/62‑1 (MQ=255)
           tgcacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAAc                                                           <  1:1607017/62‑1 (MQ=255)
           tgcacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgt                                                    >  1:1451959/1‑69 (MQ=255)
            gcacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgtt                                                   <  1:761934/69‑1 (MQ=255)
             cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGCAGGCTCAGGGAATTAACGAGACgttg                                                  >  1:2054110/1‑69 (MQ=255)
             cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttg                                                  >  1:3029579/1‑69 (MQ=255)
             cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttg                                                  >  1:2105345/1‑69 (MQ=255)
             cacatgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttg                                                  >  1:961193/1‑69 (MQ=255)
               catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttgtt                                                <  1:125740/69‑1 (MQ=255)
               catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                <  1:1582632/69‑1 (MQ=255)
               catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                <  1:2227320/69‑1 (MQ=255)
               catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                <  1:2378636/69‑1 (MQ=255)
               catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                <  1:1328788/69‑1 (MQ=255)
               catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                <  1:2131735/69‑1 (MQ=255)
               catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                <  1:649838/69‑1 (MQ=255)
               catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                <  1:3412372/69‑1 (MQ=255)
               catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                <  1:2432282/69‑1 (MQ=255)
               catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                <  1:3304916/69‑1 (MQ=255)
               catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                <  1:2620332/69‑1 (MQ=255)
               catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                <  1:2638311/69‑1 (MQ=255)
               catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                <  1:1639086/69‑1 (MQ=255)
               catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                <  1:1178303/69‑1 (MQ=255)
               catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                <  1:1790114/69‑1 (MQ=255)
               catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                <  1:2749264/69‑1 (MQ=255)
               catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                <  1:1717225/69‑1 (MQ=255)
               catgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                <  1:1003372/69‑1 (MQ=255)
                atgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttgtt                                                <  1:174110/68‑1 (MQ=255)
                atgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                <  1:2305716/68‑1 (MQ=255)
                atgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                <  1:105210/68‑1 (MQ=255)
                atgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                <  1:836142/68‑1 (MQ=255)
                 tgcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTa                                              >  1:716336/1‑69 (MQ=255)
                  gcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTAt                                             <  1:3116753/69‑1 (MQ=255)
                  gcaAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTAt                                             <  1:2082282/69‑1 (MQ=255)
                   caAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATg                                            >  1:1876879/1‑69 (MQ=255)
                   caAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAAtt                                                              >  1:1156136/1‑51 (MQ=255)
                   caAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACgag                                                        >  1:892424/1‑57 (MQ=255)
                   caAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                >  1:315360/1‑65 (MQ=255)
                   caAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                >  1:2693225/1‑65 (MQ=255)
                   caAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATg                                            >  1:2499209/1‑69 (MQ=255)
                    aaaGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                <  1:2357262/64‑1 (MQ=255)
                        caagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                >  1:253521/1‑60 (MQ=255)
                        caagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGtt                                       <  1:3003511/69‑1 (MQ=255)
                        caagcTGCTGGAGAACCGCAATAAAATGCCGAAGGCTCAGGGAATTAACGAGACgttgtt                                                >  1:227068/1‑60 (MQ=255)
                         aagcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGtt                                       <  1:2836661/68‑1 (MQ=255)
                         aagcTGCTGGAAAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGtt                                       <  1:1985527/68‑1 (MQ=255)
                         aagcTGCTGGAAAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGtt                                       <  1:3220844/68‑1 (MQ=255)
                          agcTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGtt                                       <  1:3189846/67‑1 (MQ=255)
                           gctgctGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGAt                                    <  1:2888215/69‑1 (MQ=255)
                             tgctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTa                                  <  1:855630/69‑1 (MQ=255)
                             tgctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTa                                  <  1:3336606/69‑1 (MQ=255)
                             tgctgGAGAACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTT‑ATTAc                                 >  1:1688769/1‑69 (MQ=255)
                                    gaACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTgg                            <  1:691993/68‑1 (MQ=255)
                                    gaACCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGa                           >  1:2910137/1‑69 (MQ=255)
                                     aaCCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAg                          <  1:1409843/69‑1 (MQ=255)
                                     aaCCGCAATAAAATGCTGAAAGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAg                          <  1:566847/69‑1 (MQ=255)
                                      aCCGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAg                          >  1:1284681/1‑68 (MQ=255)
                                        cGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                <  1:1229706/44‑1 (MQ=255)
                                        cGCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                <  1:1118789/44‑1 (MQ=255)
                                         gCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTg                                      >  1:3066350/1‑53 (MQ=255)
                                         gCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTg                                      >  1:2862574/1‑53 (MQ=255)
                                         gCAATAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTg                                      >  1:278204/1‑53 (MQ=255)
                                           aaTAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAg                    <  1:372902/69‑1 (MQ=255)
                                           aaTAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAg                    <  1:2202228/69‑1 (MQ=255)
                                           aaTAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAg                    <  1:2805190/69‑1 (MQ=255)
                                            aTAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttgtt                                                >  1:406786/1‑40 (MQ=255)
                                            aTAAAATGCTGAAGGCTCAGGGGATTAACGAGACgttgtt                                                >  1:271777/1‑40 (MQ=255)
                                            aTAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGtt                                       <  1:1196976/49‑1 (MQ=255)
                                            aTAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAg                    >  1:511621/1‑68 (MQ=255)
                                             tAAAATGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTg                                      >  1:2405889/1‑49 (MQ=255)
                                              aaaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaa                 >  1:1824149/1‑69 (MQ=255)
                                              aaaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaa                 <  1:2977364/69‑1 (MQ=255)
                                               aaaTGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                >  1:59039/1‑37 (MQ=255)
                                               aaaTGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                <  1:3091968/37‑1 (MQ=255)
                                               aaaTGCTGAAGGCTCAGGGAATTAACGAGACgttgtt                                                <  1:1512792/37‑1 (MQ=255)
                                               aaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGtt                                       <  1:3385874/46‑1 (MQ=255)
                                               aaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaaa                >  1:108668/1‑69 (MQ=255)
                                               aaaTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaa                 >  1:785567/1‑68 (MQ=255)
                                                 aTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCATGAAAAc              <  1:3504/69‑1 (MQ=255)
                                                 aTGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAAc              <  1:1930800/69‑1 (MQ=255)
                                                 aTGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAAc              <  1:1487818/69‑1 (MQ=255)
                                                  tGCTGAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAAc              >  1:2602542/1‑68 (MQ=255)
                                                      gAAGGCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAg         <  1:3245102/69‑1 (MQ=255)
                                                         ggCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTa                                  <  1:915972/41‑1 (MQ=255)
                                                         ggCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTa       <  1:1666993/68‑1 (MQ=255)
                                                         ggCTCAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTa       <  1:443582/68‑1 (MQ=255)
                                                             cAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaa                 >  1:1768736/1‑54 (MQ=255)
                                                             cAGGGAATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGaa                 >  1:624304/1‑54 (MQ=255)
                                                                  |                                                               
TCGTCTTTGCATGCACATGCAAAGCAAGCTGCTGGAGAACCGCAATAAAATGCTGAAGGCTCAGGGGATTAACGAGACGTTGTTTATGGCGTTGATTACGCTGGAGTCTCAGGAAAACCACAGTATTCAG  >  minE/1804024‑1804153

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