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 2,755,814 T→C 25.3% P335P (CCA→CCG)  rsmB ← 16S rRNA m5C967 methyltransferase, S‑adenosyl‑L‑methionine‑dependent

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,755,8140TC25.3% 130.6 / 41.2 110P335P (CCA→CCG) rsmB16S rRNA m5C967 methyltransferase, S‑adenosyl‑L‑methionine‑dependent
Reads supporting (aligned to +/- strand):  ref base T (65/17);  new base C (2/26);  total (67/43)
Fisher's exact test for biased strand distribution p-value = 8.66e-12
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 110 total aligned reads displayed.

CGAGAATTTCAGACTGCAATTGCGCGAGTTCCGGGATATCGCGATCGCGACGTAACCATTTAATATCTGGATGGCGACGAATCACACCGGTTGCTGAACAAGGCGCATCTAATAAAATGCGATCAAACTGT  >  minE/2755747‑2755877
                                                                   |                                                               
cGAGAATTTCAGACTGCAATTGCGCGAGTTCCGGGATATCGCGATCGCGACGTAACCATTTAATATCTg                                                                <  1:1146124/69‑1 (MQ=255)
cGAGAATTTCAGACTGCAATTGCGCGAGTTCCGGGATATCGCGATCGCGACGTAACCATTTAATATCTg                                                                <  1:3391058/69‑1 (MQ=255)
cGAGAATTTCAGACTGCAATTGCGCGAGTTCCGGGATATCGCGATCGCGACGTAACCATTTAATATCTg                                                                <  1:3037277/69‑1 (MQ=255)
 gagaATTTCAGACTTCAATTGCGCGAGTTCCGGGATATCGCGATCGCGACGTAACCATTTAATATCTgg                                                               >  1:2669844/1‑69 (MQ=255)
 gagaATTTCAGACTGCAATTGCGCGAGTTCCGGGATATCGCGATCGCGACGTAACCATTTAATATCTgg                                                               >  1:3057502/1‑69 (MQ=255)
 gagaATTTCAGACTGCAATTGCGCGAGTTCCGGGATATCGCGATCGCGACGTAACCATTTAATATCTgg                                                               >  1:2290474/1‑69 (MQ=255)
 gagaATTTCAGACTGCAATTGCGCGAGTTCCGGGATATCGCGATCGCGACGTAACCATTTAATATCTgg                                                               >  1:1642839/1‑69 (MQ=255)
          aGACTGCAATTGCGCGAGTTCCGGGATATCGCGATCGCGACGTAACCATTTAATATCTGGATGGcgacg                                                      >  1:1522164/1‑69 (MQ=255)
            aCTGCAATTGCGCGAGTTCCGGGATATCGCGATCGCGACGTAACCATTTAATATCTGGATGGcgacga                                                     <  1:3043189/68‑1 (MQ=255)
             cTGCAATTGCGCGGGTTCCGGGATATCGCGATCGCGACGTAACCATTTAATATCTGGATGGCGACGAAt                                                   <  1:1425324/69‑1 (MQ=255)
             cTGCAATTGCGCGAGTTCCGGGATATCGCGATCGCGACGTAACCATTTAATATCTGGATGGCGACGAAt                                                   <  1:2580969/69‑1 (MQ=255)
             cTGCAATTGCGCGAGTTCCGGGATATCGCGATCGCGACGTAACCATTTAATATCTGGATGGCGACGAAt                                                   <  1:2589316/69‑1 (MQ=255)
                cAACTGCGCGAGTTCTGGGATATCGCGATCGCGGCGTAACCATTTAATATCCGGATGGCGACGAATtac                                                >  1:754392/1‑69 (MQ=255)
                cAACTGCGCGAGTTCTGGGATATCGCGATCGCGGCGTAACCATTTAATATCCGGATGGCGACGAATtac                                                >  1:2794352/1‑69 (MQ=255)
                   ttGCGCGAGTTCCGGGATATCGCGATCGCGACGTAACCATTTAATATCTGGATGGCGACGAATCACAcc                                             <  1:1528293/69‑1 (MQ=255)
                     gcgcGAGTTCCGGGATATCGCGATCGCGACGTAACCATTTAATATCTGGATGGcgacga                                                     >  1:614756/1‑59 (MQ=255)
                     gcgcGAGTTCCGGGATATCGCGATCGCGACGTAACCATTTAATATCTGGATGGCGACGAATcac                                                >  1:2937785/1‑64 (MQ=255)
                     gcgcGAGTTCCGGGATATCGCGATCGCGACGTAACCATTTAATATCTGGATGGCGACGAATcac                                                >  1:2942439/1‑64 (MQ=255)
                     gcgcGAGTTCCGGGATATCGCGATCGCGACGTAACCATTTAATATCTGGATGGCGACGAATcac                                                >  1:29340/1‑64 (MQ=255)
                     gcgcGAGTTCCGGGATATCGCGATCGCGACGTAACCATTTAATATCTGGATGGCGACGAATcac                                                >  1:2764723/1‑64 (MQ=255)
                     gcgcGAGTTCCGGGATATCGCGATCGCGACGTAACCATTTAATATCTGGATGGCGACGAATcac                                                >  1:1140806/1‑64 (MQ=255)
                     gcgcGAGTTCCGGGATATCGCGATCGCGACGTAACCATTTAATATCTGGATGGCGACGAATcac                                                >  1:911598/1‑64 (MQ=255)
                     gcgcGAGTTCCGGGATATCGCGATCGCGACGTAACCATTTAATATCTGGATGGCGACGAATcac                                                >  1:3248607/1‑64 (MQ=255)
                     gcgcGAGTTCCGGGATATCGCGATCGCGACGTAACCATTTAATATCTGGATGGCGACGAATcac                                                >  1:2371572/1‑64 (MQ=255)
                     gcgcGAGTTCCGGGATATCGCGATCGCGACGTAACCATTTAATATCTGGATGGCGACGAATcac                                                >  1:3377268/1‑64 (MQ=255)
                     gcgcGAGTTCCGGGATATCGCGATCGCGACGTAACCATTTAATATCTGGATGGCGACGAATcac                                                >  1:1249287/1‑64 (MQ=255)
                     gcgcGAGTTCCGGGATATCGCGATCGCGACGTAACCATTTAATATCTGGATGGCGACGAATcac                                                >  1:2111253/1‑64 (MQ=255)
                     gcgcGAGTTCCGGGATATCGCGATCGCGACGTAACCATTTAATATCTGGATGGCGACGAATcac                                                <  1:1677300/64‑1 (MQ=255)
                     gcgcGAGTTCCGGGATATCGCGATCGCGACGTAACCATTTAATATCTGGATGGCGACGAATcac                                                >  1:69084/1‑64 (MQ=255)
                      cgcgAGTTCCGGGATATCGCGATCGCGACGTAACCATTTAATATCTGGATGGCGACGAATcac                                                <  1:1356046/63‑1 (MQ=255)
                            ttCCGGGAGATCGCGATCGCGACGTAACCATTTAATATCTGGATGGCGACGAATCACACCGGTTGCTGa                                    <  1:414629/69‑1 (MQ=255)
                                   atatCGCGATCGCGACGTAACCATTTAATATCTGGATGGCGACGAATCACACCGGTTGCTGAACAAgg                              >  1:1563960/1‑68 (MQ=255)
                                   atatCGCGATCGCGACGTAACCATTTAATATCTGGATGGCGACGAATCACACCGGTTGCTGAACAAgg                              >  1:2460745/1‑68 (MQ=255)
                                   atatCGCGATCGCGACGTAACCATTTAATATCTGGATGGCGACGAATCACACCGGTTGCTGAACAAgg                              >  1:1911823/1‑68 (MQ=255)
                                   atatCGCGATCGCGACGTAACCATTTAATATCTGGATGGCGACGAATCACACCGGTTGCTGAACAAgg                              >  1:3075880/1‑68 (MQ=255)
                                   atatCGCGATCGCGACGTAACCATTTAATATCTGGATGGCGACGAATCACACCGGTTGCTGAACAAgg                              >  1:2064445/1‑68 (MQ=255)
                                   atatCGCGATCGCGACGTAACCATTTAATATCTGGATGGCGACGAATCACACCGGTTGCTGAACAAg                               >  1:2977746/1‑67 (MQ=255)
                                     atcgcgatcgcgACGTAACCATTTAATATCTGGATGTCGACGAATCACACCGGTTGCTGAACAAGgcgc                           >  1:3234543/1‑69 (MQ=255)
                                     atcgcgatcgcgACGTAACCATTTAATATCTGGATGGCGACGAATCACACCGGTTGCTGAACAAGgcgc                           >  1:1302462/1‑69 (MQ=255)
                                     atcgcgatcgcgACGTAACCATTTAATATCTGGATGGCGACGAATCACACCGGTTGCTGAACAAGgcgc                           >  1:3210368/1‑69 (MQ=255)
                                     atcgcgatcgcgACGTAACCATTTAATATCTGGATGGCGACGAATCACACCGGTTGCTGAACAAGgcgc                           >  1:635749/1‑69 (MQ=255)
                                     atcgcgatcgcgACGTAACCATTTAATATCTGGATGGCGACGAATCACACCGGTTGCTGAACAAGgcgc                           >  1:3104930/1‑69 (MQ=255)
                                     atcgcgatcgcgACGTAACCATTTAATATCTGGATGGCGACGAATCACACCGGTTGCTGAACAAGgcgc                           >  1:1403579/1‑69 (MQ=255)
                                     atcgcgatcgcgACGTAACCATTTAATATCTGGATGGCGACGAATCACACCGGTTGCTGAACAAGgcgc                           >  1:2725387/1‑69 (MQ=255)
                                     atcgcgatcgcgACGTAACCATTTAATATCTGGATGGCGACGAATCACACCGGTTGCTGAACAAGgcgc                           >  1:2710712/1‑69 (MQ=255)
                                     atcgcgatcgcgACGTAACCATTTAATATCTGGATGGCGACGAATCACACCGGTTGCTGAACAAGgcgc                           >  1:1334663/1‑69 (MQ=255)
                                     atcgcgatcgcgACGTAACCATTTAATATCTGGATGGCGACGAATCACACCGGTTGCTGAACAAGgcgc                           >  1:3175598/1‑69 (MQ=255)
                                     atcgcgatcgcgACGTAACCATTTAATATCTGGATGGCGACGAATCACACCGGTTGCTGAACAAGgcgc                           >  1:591771/1‑69 (MQ=255)
                                     atcgcgatcgcgACGTAACCATTTAATATCTGGATGGCGACGAATCACACCGGTTGCTGAACAAGgcgc                           >  1:2487044/1‑69 (MQ=255)
                                     atcgcgatcgcgACGTAACCATTTAATATCTGGATGGCGACGAATCACACCGGTTGCTGAACAAGgcgc                           >  1:2463783/1‑69 (MQ=255)
                                     atcgcgatcgcgACGTAACCATTTAATATCTGGATGGCGACGAATCACACCGGTTGCTGAACAAGgcgc                           >  1:557439/1‑69 (MQ=255)
                                     atcgcgatcgcgACGTAACCATTTAATATCTGGATGGCGACGAATCACACCGGTTGCTGAACAAGgcgc                           >  1:2355250/1‑69 (MQ=255)
                                     atcgcgatcgcgACGTAACCATTTAATATCTGGATGGCGACGAATCACACCGGTTGCTGAACAAGgcgc                           >  1:221221/1‑69 (MQ=255)
                                     atcgcgatcgcgACGTAACCATTTAATATCTGGATGGCGACGAATCACACCGGTTGCTGAACAAGgcgc                           >  1:2173801/1‑69 (MQ=255)
                                     atcgcgatcgcgACGTAACCATTTAATATCTGGATGGCGACGAATCACACCGGTTGCTGAACAAGgcg                            >  1:3154101/1‑68 (MQ=255)
                                     atcgcgatcgcgACGTAACCATTTAATATCTGGATGGCGACGAATCACACCGGTTGCTGAACAAGgcg                            >  1:489230/1‑68 (MQ=255)
                                     atcgcgatcgcgACGTAACCATTTAATATCTGGATGGCGACGAATCACACCGGTTGCTGAACAAGgcg                            >  1:1835370/1‑68 (MQ=255)
                                     atcgcgatcgagACGTAACCATTTAATATCTGGATGGCGACGAATCACACCGGATGCTGaa                                   >  1:2513402/1‑61 (MQ=255)
                                      tcgcgatcgcgaCGTAACCATTTAATATCTGGATGGCGACGAATCACACCGGTTGCTGAACAAGGCGCa                          >  1:3109047/1‑69 (MQ=255)
                                      tcgcgatcgcgaCGTAACCATTTAATATCTGGATGGCGACGAATCACACCGGTTGCTGAACAAGGCGCa                          >  1:3261481/1‑69 (MQ=255)
                                      tcgcgatcgcgaCGTAACCATTTAATATCTGGATGGCGACGAATCACACCGGTTGCTGAACAAGGCGCa                          >  1:535218/1‑69 (MQ=255)
                                      tcgcgatcgcgaCGTAACCATTTAATATCTGGATGGCGACGAATCACACCGGTTGCTGAACAAGGCGCa                          >  1:394656/1‑69 (MQ=255)
                                      tcgcgatcgcgaCGTAACCATTTAATATCTGGATGGCGACGAATCACACCGGTTGCTGAACAAGGCGCa                          >  1:1437067/1‑69 (MQ=255)
                                      tcgcgatcgcgaCGTAACCATTTAATATCTGGATGGCGACGAATCACACCGGTTGCTGAACAAGGCGCa                          >  1:2936247/1‑69 (MQ=255)
                                      tcgcgatcgcgaCGTAACCATTTAATATCTGGATGGCGACGAATCACACCGGTTGCTGAACAAGGCGCa                          >  1:242978/1‑69 (MQ=255)
                                      tcgcgatcgcgaCGTAACCATTTAATATCTGGATGGCGACGAATCACACCGGTTGCTGAACAAGGCGCa                          >  1:1794556/1‑69 (MQ=255)
                                      tcgcgatcgcgaCGTAACCATTTAATATCTGGATGGCGACGAATCACACCGGTTGCTGAACAAGGCGCa                          >  1:2764088/1‑69 (MQ=255)
                                      tcgcgatcgcgaCGTAACCATTTAATATCTGGATGGCGACGAATCACACCGGTTGCTGAACAAGGCGCa                          >  1:2517991/1‑69 (MQ=255)
                                        gcgatcgcggCGTAACCATTTAATATCCGGATGGCGACGAATTACACCAGTTGCCGAACa                                 <  1:236135/60‑1 (MQ=255)
                                        gcgatcgcggCGTAACCATTTAATATCCGGATGGCGACGAATTACACCAGTTGCCGAACa                                 <  1:2912977/60‑1 (MQ=255)
                                        gcgatcgcggCGTAACCATTTAATATCCGGATGGCGACGAATTACACCAGTTGCCGAACa                                 <  1:3383118/60‑1 (MQ=255)
                                        gcgatcgcggCGTAACCATTTAATATCCGGATGGCGACGAATTACACCAGTTGCCGAACa                                 <  1:2344218/60‑1 (MQ=255)
                                        gcgatcgcggCGTAACCATTTAATATCCGGATGGCGACGAATTACACCAGTTGCCGAACa                                 <  1:2257990/60‑1 (MQ=255)
                                        gcgatcgcggCGTAACCATTTAATATCCGGATGGCGACGAATTACACCAGTTGCCGAACa                                 <  1:919814/60‑1 (MQ=255)
                                        gcgatcgcggCGTAACCATTTAATATCCGGATGGCGACGAATTACACCAGTTGCCGAACa                                 <  1:2095608/60‑1 (MQ=255)
                                        gcgatcgcggCGTAACCATTTAATATCCGGATGGCGACGAATTACACCAGTTGCCGAACa                                 <  1:1934322/60‑1 (MQ=255)
                                        gcgatcgcggCGTAACCATTTAATATCCGGATGGCGACGAATTACACCAGTTGCCGAACa                                 <  1:1699373/60‑1 (MQ=255)
                                        gcgatcgcggCGTAACCATTTAATATCCGGATGGCGACGAATTACACCAGTTGCCGAACa                                 <  1:1472692/60‑1 (MQ=255)
                                        gcgatcgcggCGTAACCATTTAATATCCGGATGGCGACGAATTACACCAGTTGCCGAACa                                 <  1:902406/60‑1 (MQ=255)
                                        gcgatcgcggCGTAACCATTTAATATCCGGATGGCGACGAATTACACCAGTTGCCGAACa                                 <  1:1410597/60‑1 (MQ=255)
                                        gcgatcgcggCGTAACCATTTAATATCCGGATGGCGACGAATTACACCAGTTGCCGAACa                                 <  1:3359953/60‑1 (MQ=255)
                                        gcgatcgcggCGTAACCATTTAATATCCGGATGGCGACGAATTACACCAGTTGCCGAACa                                 <  1:3324526/60‑1 (MQ=255)
                                        gcgatcgcggCGTAACCATTTAATATCCGGATGGCGACGAATTACACCAGTTGCCGAACa                                 <  1:2369190/60‑1 (MQ=255)
                                        gcgatcgcggCGTAACCATTTAATATCCGGATGGCGACGAATTACACCAGTTGCCGAACa                                 <  1:2535010/60‑1 (MQ=255)
                                        gcgatcgcggCGTAACCATTTAATATCCGGATGGCGACGAATTACACCAGTTGCCGAACa                                 <  1:1351504/60‑1 (MQ=255)
                                        gcgatcgcggCGTAACCATTTAATATCCGGATGGCGACGAATTACACCAGTTGCCGAACa                                 <  1:2606884/60‑1 (MQ=255)
                                        gcgatcgcggCGTAACCATTTAATATCCGGATGGCGACGAATTACACCAGTTGCCGAACa                                 <  1:126830/60‑1 (MQ=255)
                                        gcgatcgcggCGTAACCATTTAATATCCGGATGGCGACGAATTACACCAGTTGCCGAACa                                 <  1:2834902/60‑1 (MQ=255)
                                        gcgatcgcggCGTAACCATTTAATATCCGGATGGCGACGAATTACACCAGTTGCCGAACa                                 <  1:1320782/60‑1 (MQ=255)
                                        gcgatcgcggCGTAACCATTTAATATCCGGATCGCGACGAATTACACCAGTTGCCGAACa                                 <  1:1659575/60‑1 (MQ=255)
                                        gcgatcgcgaCGTAACCATTTAATATCTGGATGGCGACGAATCACACCGGTTGCTGAACAAGGCGCAt                         >  1:3043446/1‑68 (MQ=255)
                                        gcgatcgcgaCGTAACCATTTAATATCTGGATGGCGACGAATCACACCGGTTGCTGAACAAGGCGCAt                         >  1:867241/1‑68 (MQ=255)
                                          gatcgcggCGTAACCATTTAATATCCGGATGGCGACGAATTACACCAGTTGCCGAACa                                 <  1:1368364/58‑1 (MQ=255)
                                           atcgcggCGTAACCATTTAATATCCGGATCGCGACGAATTACACCAGTTGCCGAACa                                 <  1:2815473/57‑1 (MQ=255)
                                                            tAATATCTGGATGGCGACGAATCACACCGGTTGCTGAACAAGGCGCATCTAATAAAATGCGATCAAACt    >  1:2664407/1‑69 (MQ=255)
                                                            tAATATCTGGATGGCGACGAATCACACCGGTTGCTGAACAAGGCGCATCTAATAAAATGCGATCAAACt    >  1:2562281/1‑69 (MQ=255)
                                                            tAATATCTGGATGGCGACGAATCACACCGGTTGCTGAACAAGGCGCATCTAATAAAATGCGATCAAACt    >  1:2102809/1‑69 (MQ=255)
                                                               tatCTGGATGGCGACGAATCACACCGGTTGCTGAACAAGGCGCATCTAATAAAATGCGATCAAACTg   <  1:915206/67‑1 (MQ=255)
                                                               tatCTGGATGGCGACGAATCACACCGGTTGCTGAACAAGGCGCATCTAATAAAATGCGATCAAACTGt  <  1:703389/68‑1 (MQ=255)
                                                                atCTGGATGGCGACGAATCACACCGGTTGCTGAACAAGGCGCATCTAATAAAATGCGATCAAACTGt  <  1:964011/67‑1 (MQ=255)
                                                                   |                                                               
CGAGAATTTCAGACTGCAATTGCGCGAGTTCCGGGATATCGCGATCGCGACGTAACCATTTAATATCTGGATGGCGACGAATCACACCGGTTGCTGAACAAGGCGCATCTAATAAAATGCGATCAAACTGT  >  minE/2755747‑2755877

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