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 2,457,681 A→G 30.3% K131K (AAA→AAG)  yieP → predicted transcriptional regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,457,6810AG30.3% 92.4 / 48.6 102K131K (AAA→AAG) yiePpredicted transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base A (39/32);  new base G (16/15);  total (55/47)
Fisher's exact test for biased strand distribution p-value = 8.30e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.89e-01

Only 100 of 107 total aligned reads displayed.

ATGCGTATCTGTCTGGAGCCGCAAGCCTGCCTACTGGCAGCAACGGTTGGCACCGCGGAACAGAAAGCGCATCTCAATACGTTAATGGCCGAAATGGCGGCATTAAAAGAGAACTTTCGCCGTGAACGC  >  minE/2457616‑2457744
                                                                 |                                                               
aTGCGTATCTGTCTGGAGCCGCAAGCCTGCCTACTGGCAGCAACGGTTGGCACCGCGGAACAGAAAgcg                                                              >  1:2174837/1‑69 (MQ=255)
aTGCGTATCTGTCTGGAGCCGCAAGCCTGCCTACTGGCAGCAACGGTTGGCACCGCGGAACAGAAAgcg                                                              >  1:1859645/1‑69 (MQ=255)
aTGCGTATCTGTCTGGAGCCGCAAGCCTGCCTACTGGCAGCAACGGTTGGCACCGCGGAACAGAAAgcg                                                              >  1:1305897/1‑69 (MQ=255)
aTGCGTATCTGTCTGGAGCCGCAAGCCTGCCTACTGGCAGCAACGGTTGGCACCGCGGAACAGAAAgcg                                                              >  1:1661150/1‑69 (MQ=255)
aTGCGTATCTGTCTGGAGCCGCAAGCCTGCCTACTGGCAGCAACGGTTGGCACCGCGGAACAGAAAgcg                                                              >  1:1794890/1‑69 (MQ=255)
aTGCGTATCTGTCTGGAGCCGCAAGCCTGCCTACTGGCAGCAACGGTTGGCACCGCGGAACAGAAAgc                                                               >  1:182966/1‑68 (MQ=255)
   cGTATCTGTCTGGAGCCGCAAGCCTGCCTACTGGCAGCAACGGTTGGCACCGCGGAACAGAAAGCGCa                                                            >  1:2175673/1‑68 (MQ=255)
   cGTATCTGTCTGGAGCCGCAAGCCTGCCTACTGGCAGCAACGGTTGGCACCGCGGAACAGAAAGCGCa                                                            >  1:2897302/1‑68 (MQ=255)
   cGTATCTGTCTGGAGCCGCAAGCCTGCCTACTGGCAGCAACGGTTGGCACCGCGGAACAGAAAGCGCAt                                                           >  1:2798793/1‑69 (MQ=255)
   cGTATCTGTCTGGAGCCGCAAGCCTGCCTACTGGCAGCAACGGTTGGCACCGCGGAACAGAAAGCGCAt                                                           >  1:879170/1‑69 (MQ=255)
   cGTATCTGTCTGGAGCCGCAAGCCTGCCTACTGGCAGCAACGGTTGGCACCGCGGAACAGAAAGCGCAt                                                           >  1:881389/1‑69 (MQ=255)
      aTCTGTCTGGAGCCGCAAGCCTGCCTACTGGCAGCAACGGTTGGCACCGCGGAACAGAAAGCGCAtctc                                                        <  1:787622/69‑1 (MQ=255)
      aTCTGTCTGGAGCCGCAAGCCTGCCTACTGGCAGCAACGGTTGGCACCGCGGAACAGAAAGCGCAtctc                                                        <  1:170972/69‑1 (MQ=255)
      aTCTGTCTGGAGCCGCAAGCCTGCCTACTGGCAGCAACGGTTGGCACCGCGGAACAGAAAGCGCAtctc                                                        <  1:3384460/69‑1 (MQ=255)
      aTCTGTCTGGAGCCGCAAGCCTGCCTACTGGCAGCAACGGTTGGCACCGCGGAACAGAAAGCGCAtctc                                                        <  1:3380555/69‑1 (MQ=255)
      aTCTGTCTGGAGCCGCAAGCCTGCCTACTGGCAGCAACGGTTGGCACCGCGGAACAGAAAGCGCAtctc                                                        <  1:1791815/69‑1 (MQ=255)
      aTCTGTCTGGAGCCGCAAGCCTGCCTACTGGCAGCAACGGTTGGCACCGCGGAACAGAAAGCGCAtctc                                                        <  1:139144/69‑1 (MQ=255)
      aTCTGTCTGGAGCCGCAAGCCTGCCTACTGGCAGCAACGGTTGGCACCGCGGAACAGAAAGCGCAtctc                                                        <  1:3337246/69‑1 (MQ=255)
      aTCTGTCTGGAGCCGCAAGCCTGCCTACTGGCAGCAACGGTTGGCACCGCGGAACAGAAAGCGCAtctc                                                        <  1:3249153/69‑1 (MQ=255)
      aTCTGTCTGGAGCCGCAAGCCTGCCTACTGGCAGCAACGGTTGGCACCGCGGAACAGAAAGCGCAtctc                                                        <  1:1957864/69‑1 (MQ=255)
      aTCTGTATGGAGCCGCAAGCCTGCCTACTGGCAGCAACGGTTGGCACCGCGGAACAGAAAGCGCAtctc                                                        <  1:2078249/69‑1 (MQ=255)
       tctgtctgGAGCCGCAAGCCTGCCTACTGGCAGCAACGGTTGGCACCGCGGAACAGAAAGCGCAtctc                                                        <  1:2982365/68‑1 (MQ=255)
         tgtctgGAGCCGCAAGCCTGCCTACTGGCAGCAACGGTTGGCACCGCGGAACAGAAAGCGCATCTCAAt                                                     >  1:1763912/1‑69 (MQ=255)
         tgtctgGAGCCGCAAGCCTGCCTACTGGCAGCAACGGTTGGCACCGCGGAACAGAAAGCGCATCTCAAt                                                     >  1:1345425/1‑69 (MQ=255)
         tgtctgGAGCCGCAAGCCTGCCTACTGGCAGCAACGGTTGGCACCGCGGAACAGAAAGCGCATCTCAAt                                                     >  1:2907992/1‑69 (MQ=255)
             tgGAGCCGCAAGCCTGCCTACTGGCAGCAACGGTTGGCACCGCGGAACAGAAAgc                                                               >  1:2963653/1‑55 (MQ=255)
             tgGAGCCGCAAGCCTGCCTACTGGCAGCAACGGTTGGCACCGCGGAACAGAAAGCGCATCTCAATAc                                                   >  1:2889395/1‑67 (MQ=255)
             tgGAGCCGCAAGCCTGCCTACTGGCAGCAACGGTTGGCACCGCGGAACAGAAAGCGCATCTCAATACg                                                  >  1:2200899/1‑68 (MQ=255)
             tgGAGCCGCAAGCCTGCCTACTGGCAGCAACGGTTGGCACCGCGGAACAGAAAGCGCATCTCAATACg                                                  >  1:3342440/1‑68 (MQ=255)
             tgGAGCCGCAAGCCTGCCTACTGGCAGCAACGGTTGGCACCGCGGAACAGAAAGCGCATCTCAATACg                                                  >  1:2613205/1‑68 (MQ=255)
             tgGAGCCGCAAGCCTGCCTACTGGCAGCAACGGTTGGCACCGCGGAACAGAAAGCGCATCTCAATACg                                                  >  1:2148370/1‑68 (MQ=255)
             tgGAGCCGCAAGCCTGCCTACTGGCAGCAACGGTTGGCACCGCGGAACAGAAAGCGCATCTCAATACg                                                  >  1:900344/1‑68 (MQ=255)
             tgGAGCCGCAAGCCTGCCTACTGGCAGCAACGGTTGGCACCGCGGAACAGAAAGCGCATCTCAATACg                                                  >  1:2076586/1‑68 (MQ=255)
             tgGAGCCGCAAGCCTGCCTACTGGCAGCAACGGTTGGCACCGCGGAACAGAAAGCGCATCTCAATACg                                                  >  1:1389403/1‑68 (MQ=255)
             tgGAGCCGCAAGCCTGCCTACTGGCAGCAACGGTTGGCACCGCGGAACAGAAAGCGCATCTCAATACg                                                  >  1:77984/1‑68 (MQ=255)
             tgGAGCCGCAAGCCTGCCTACTGGCAGCAACGGTTGGCACCGCGGAACAGAAAGCGCATCTCAATACg                                                  >  1:149260/1‑68 (MQ=255)
             tgGAGCCGCAAGCCTGCCTACTGGCAGCAACGGTTGGCACCGCGGAACAGAAAGAGCATCTCAATACg                                                  >  1:1338836/1‑68 (MQ=255)
                 gCCTCAAGCCTGCCTACTGGCAGCAACGGTTGGCACCGCGGAACAGAAAGCGCATCTCAATACGtt                                                <  1:3175750/66‑1 (MQ=255)
                 gCCGCAAGCCTGCCTACTGGCAGCAACGGTTGGCACCGCGGAACAGAAAGCGCATCTCAATACGtt                                                <  1:2252304/66‑1 (MQ=255)
                 gCCGCAAGCCTGCCTACTGGCAGCAACGGTTGGCACCGCGGAACAGAAAGCGCATCTCAATACGtt                                                <  1:2583699/66‑1 (MQ=255)
                 gCCGCAAGCCTGCCTACTGGCAGCAACGGTTGGCACCGCGGAACAGAAAGCGCATCTCAATACGtt                                                <  1:1661507/66‑1 (MQ=255)
                 gCCGCAAGCCTGCCTACTGGCAGCAACGGTTGGCACCGCGGAACAGAAAGCGCATCTCAATACGtt                                                <  1:286758/66‑1 (MQ=255)
                 gCCGCAAGCCTGCCTACTGGCAGCAACGGTTGGCACCGCGGAACAGAAAGCGCATCTCAATACGtt                                                <  1:2919798/66‑1 (MQ=255)
                 gCCGCAAGCCTGCCTACTGGCAGCAACGGTTGGCACCGCGGAACAGAAAGCGCATCTCAATACGtt                                                <  1:1097783/66‑1 (MQ=255)
                       aGCCTGCCTACTGGCAGCAACGGTTGGCACCGCGGAACAGAAAGCGCATCTCAATACGTTAATGGCCGa                                       <  1:1421243/69‑1 (MQ=255)
                       aGCCTGCCTACTGGCAGCAACGGTTGGCACCGCGGAACAGAAAGCGCATCTCAATACGTTAATGGCCGa                                       <  1:2758355/69‑1 (MQ=255)
                       aGCCTGCCTACTGGCAGCAACGGTTGGCACCGCGGAACAGAAAGCGCATCTCAATACGTTAATGGCCGa                                       <  1:3282976/69‑1 (MQ=255)
                       aGCCTGCCTACTGGCAGCAACGGTTGGCACCGCGGAACAGAAAGCGCATCTCAATACGTTAATGGCCGa                                       <  1:895560/69‑1 (MQ=255)
                       aGCCTGCCTACTGGCAGCAACGGTTGGCACCGCGGAACAGAAAGCGCATCTCAATACGTTAATGGCCGa                                       <  1:1445497/69‑1 (MQ=255)
                       aGCCTGCCTACTGGCAGCAACGGTTGGCACCGCGGAACAGAAAGCGCATCTCAATACGTTAATGGCCGa                                       <  1:38817/69‑1 (MQ=255)
                       aGCCTGCCTACTGGCAGCAACGGTTGGCACCGCGGAACAGAAAGCGCATCTCAATACGTTAATGGCCGa                                       <  1:43500/69‑1 (MQ=255)
                        gcctgcctACTGGCAGCAACGGTTGGCACCGCGGAACAGAAAGCGCATCTCAATACGTTAACGGCCGa                                       <  1:2744777/68‑1 (MQ=255)
                                          aCGGTTGGCACCGCGGAACAGAAAGCGCATCTCAATACGTTAATGGCCGAAATGGCGGCATTAAAagag                    >  1:2118659/1‑69 (MQ=255)
                                           aggTTGGCACCGCGGAACAGAAGGCGCATCTCAATACGTTa                                               >  1:283747/2‑41 (MQ=39)
                                           aggTTGGCACCGCGGAACAGAAGGCGCATCTCAATACGTTa                                               >  1:2103333/2‑41 (MQ=39)
                                           aggTTGGCACCGCGGAACAGAAGGCGCATCTCAATACGTTa                                               >  1:301868/2‑41 (MQ=39)
                                           aggTTGGCACCGCGGAACAGAAGGCGCATCTCAATACGTTa                                               >  1:1111142/2‑41 (MQ=39)
                                           aggTTGGCACCGCGGAACAGAAGGCGCATCTCAATACGTTa                                               >  1:817373/2‑41 (MQ=39)
                                           aggTTGGCACCGCGGAACAGAAGGCGCATCTCAATACGTTa                                               >  1:2890796/2‑41 (MQ=39)
                                           aggTTGGCACCGCGGAACAGAAGGCGCATCTCAATACGTTa                                               >  1:1257145/2‑41 (MQ=39)
                                           aggTTGGCACCGCGGAACAGAAGGCGCATCTCAATACGTTa                                               >  1:1333969/2‑41 (MQ=39)
                                           aggTTGGCACCGCGGAACAGAAGGCGCATCTCAATACGTTa                                               >  1:2511258/2‑41 (MQ=39)
                                           aggTTGGCACCGCGGAACAGAAGGCGCATCTCAATACGTTa                                               >  1:2258342/2‑41 (MQ=39)
                                           aggTTGGCACCGCGGAACAGAAGGCGCATCTCAATACGTTa                                               >  1:2776016/2‑41 (MQ=39)
                                           aggTTGGCACCGCGGAACAGAAGGCGCATCTCAATACGTTa                                               >  1:2683240/2‑41 (MQ=39)
                                           aggTTGGCACCGCGGAACAGAAGGCGCATCTCAATACGTTa                                               >  1:2415535/2‑41 (MQ=39)
                                           aggTTGGCACCGCGGAACAGAAGGCGCATCTCAATACGTTa                                               >  1:4581/2‑41 (MQ=39)
                                           aggTTGGCACCGCGGAACAGAAGGCGCATCTCAATACGTTa                                               >  1:245750/2‑41 (MQ=39)
                                              ttcgCACCGCGGAACAGAAGCCGCATCTCAATACGTTAATGGCCGAAATGGCGGCATTAAAAGAGAACt                <  1:499557/66‑1 (MQ=255)
                                              ttGGCACCGCGGAACAGAAGGCGCATCTCAATACGTTAATGGCCGAAATGGCGGCATTAAAAGAGAACt                <  1:3388910/69‑1 (MQ=255)
                                              ttGGCACCGCGGAACAGAAGGCGCATCTCAATACGTTAATGGCCGAAATGGCGGCATTAAAAGAGAACt                <  1:257202/69‑1 (MQ=255)
                                              ttGGCACCGCGGAACAGAAGGCGCATCTCAATACGTTAATGGCCGAAATGGCGGCATTAAAAGAGAACt                <  1:3338297/69‑1 (MQ=255)
                                              ttGGCACCGCGGAACAGAAGGCGCATCTCAATACGTTAATGGCCGAAATGGCGGCATTAAAAGAGAACt                <  1:2212215/69‑1 (MQ=255)
                                              ttGGCACCGCGGAACAGAAGGCGCATCTCAATACGTTAATGGCCGAAATGGCGGCATTAAAAGAGAACt                <  1:1076188/69‑1 (MQ=255)
                                              ttGGCACCGCGGAACAGAAGGCGCATCTCAATACGTTAATGGCCGAAATGGCGGCATTAAAAGAGAACt                <  1:1453825/69‑1 (MQ=255)
                                              ttGGCACCGCGGAACAGAAGGCGCATCTCAATACGTTAATGGCCGAAATGGCGGCATTAAAAGAGAACt                <  1:1748181/69‑1 (MQ=255)
                                              ttGGCACCGCGGAACAGAAGGCGCATCTCAATACGTTAATGGCCGAAATGGCGGCATTAAAAGAGAACt                <  1:2345842/69‑1 (MQ=255)
                                              ttGGCACCGCGGAACAGAAGGCGCATCTCAATACGTTAATGGCCGAAATGGCGGCATTAAAAGAGAACt                <  1:2511981/69‑1 (MQ=255)
                                              ttGGCACCGCGGAACAGAAGGCGCATCTCAATACGTTAATGGCCGAAATGGCGGCATTAAAAGAGAACt                <  1:262299/69‑1 (MQ=255)
                                              ttGGCACCGCGGAACAGAAGGCGCATCTCAATACGTTAATGGCCGAAATGGCGGCATTAAAAGAGAACt                <  1:2859764/69‑1 (MQ=255)
                                                       cgGAACAGAAAGCGCATCTCAATACGTTAATGGCCGAAATGGCGGCATTAAAAGAGAACTTTCGCCGTg       <  1:2014630/69‑1 (MQ=255)
                                                       cgGAACAGAAAGCGCATCTCAATACGTTAATGGCCGAAATGGCGGCATTAAAAGAGAACTTTCGCCGTg       <  1:1941412/69‑1 (MQ=255)
                                                       cgGAACAGAAAGCGCATCTCAATACGTTAATGGCCGAAATGGCGGCATTAAAAGAGAACTTTCGCCGTg       <  1:2288181/69‑1 (MQ=255)
                                                            cAGAAAGCGCATCTCAATACGTTAATGGCCGAAATGGCGGCATTAAAAGAGAACTTTCGCCGTGACCg   >  1:3103625/1‑68 (MQ=255)
                                                            cAGAAAGCGCATCTCAATACGTTAATGGCCGAAATGGCGGCATTAAAAGAGAACTTTCGCCGTGAACGc  >  1:3019740/1‑69 (MQ=255)
                                                            cAGAAAGCGCATCTCAATACGTTAATGGCCGAAATGGCGGCATTAAAAGAGAACTTTCGCCGTGAACGc  >  1:347126/1‑69 (MQ=255)
                                                            cAGAAAGCGCATCTCAATACGTTAATGGCCGAAATGGCGGCATTAAAAGAGAACTTTCGCCGTGAACGc  >  1:1148279/1‑69 (MQ=255)
                                                            cAGAAAGCGCATCTCAATACGTTAATGGCCGAAATGGCGGCATTAAAAGAGAACTTTCGCCGTGAACGc  >  1:437392/1‑69 (MQ=255)
                                                            cAGAAAGCGCATCTCAATACGTTAATGGCCGAAATGGCGGCATTAAAAGAGAACTTTCGCCGTGAACGc  >  1:2099611/1‑69 (MQ=255)
                                                            cAGAAAGCGCATCTCAATACGTTAATGGCCGAAATGGCGGCATTAAAAGAGAACTTTCGCCGTGAACGc  >  1:1005473/1‑69 (MQ=255)
                                                            cAGAAAGCGCATCTCAATACGTTAATGGCCGAAATGGCGGCATTAAAAGAGAACTTTCGCCGTGAACGc  >  1:2358178/1‑69 (MQ=255)
                                                            cAGAAAGCGCATCTCAATACGTTAATGGCCGAAATGGCGGCATTAAAAGAGAACTTTCGCCGTGAACGc  >  1:766209/1‑69 (MQ=255)
                                                            cAGAAAGCGCATCTCAATACGTTAATGGCCGAAATGGCGGCATTAAAAGAGAACTTTCGCCGTGAACGc  >  1:3306524/1‑69 (MQ=255)
                                                            cAGAAAGCGCATCTCAATACGTTAATGGCCGAAATGGCGGCATTAAAAGAGAACTTTCGCCGTGAACGc  >  1:1505024/1‑69 (MQ=255)
                                                            cAGAAAGCGCATCTCAATACGTTAATGGCCGAAATGGCGGAATTAAAAGAGAACTTTCGCCGTGAACGc  >  1:679802/1‑69 (MQ=255)
                                                                aaGCGCATCTCAATACGTTAATGGCCGAAATGGCGGCATTAAAAgaga                   <  1:2738213/48‑1 (MQ=255)
                                                                aaGCGCATCTCAATACGTTAATGGCCGAAATGGCGGCATTAAAAgaga                   <  1:1783430/48‑1 (MQ=255)
                                                                aaGCGCATCTCAATACGTTAATGGCCGAAATGGCGGCATTAAAAgaga                   <  1:589718/48‑1 (MQ=255)
                                                                aaGCGCATCTCAATACGTTAATGGCCGAAATGGCGGCATTAAAAgaga                   <  1:2269705/48‑1 (MQ=255)
                                                                aaGCGCATCTCAATACGTTAATGGCCGAAATGGCGGCATTAAAAgaga                   <  1:3405362/48‑1 (MQ=255)
                                                                 |                                                               
ATGCGTATCTGTCTGGAGCCGCAAGCCTGCCTACTGGCAGCAACGGTTGGCACCGCGGAACAGAAAGCGCATCTCAATACGTTAATGGCCGAAATGGCGGCATTAAAAGAGAACTTTCGCCGTGAACGC  >  minE/2457616‑2457744

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