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 2,482,189 T→C 45.5% S225S (TCA→TCG)  mdtL ← multidrug efflux system protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,482,1890TC45.5% 15.8 / 94.0 112S225S (TCA→TCG) mdtLmultidrug efflux system protein
Reads supporting (aligned to +/- strand):  ref base T (29/32);  new base C (7/44);  total (36/76)
Fisher's exact test for biased strand distribution p-value = 2.03e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 117 total aligned reads displayed.

TCAGCGCCATAATGGTGGCGTATTCACCGCGCTCAAACCCCATGATTTCCATCAGCAATACCGGTGACGTGTTGACGAAAGTGAGGATCACCGAAACGCTGAGGGTGGTGATAACAACACGGCTGAGGAAAA  >  minE/2482125‑2482256
                                                                |                                                                   
tCAGCGCCATAATGGTGGCGTATTCACCGCGCTCAAACCCCATGATTTCCATCAGCAATACCGTTGACg                                                                 <  1:1329771/69‑1 (MQ=255)
tCAGCGCCATAATGGTGGCGTATTCACCGCGCTCAAACCCCATGATTTCCATCAGCAATACCGGTGACg                                                                 <  1:1018996/69‑1 (MQ=255)
tCAGCGCCATAATGGTGGCGTATTCACCGCGCTCAAACCCCATGATTTCCATCAGCAATACCGGTGACg                                                                 <  1:253401/69‑1 (MQ=255)
tCAGCGCCATAATGGTGGCGTATTCACCGCGCTCAAACCCCATGATTTCCATCAGCAATACCGGTGACg                                                                 <  1:1506291/69‑1 (MQ=255)
 cAGCGCCATAATGGTGGCGTATTCACCGCGCTCAAACCCCATGATTTCCATCAGCAATACCGGTGACg                                                                 <  1:2836380/68‑1 (MQ=255)
           aTGGTGGCGTATTCACCGCGCTCAAACCCCATGATTTCCATCAGCAATACCGGTGACGTGTTGACGaa                                                       >  1:1975415/1‑68 (MQ=255)
             ggtggCGTATTCACCGCGCTCAAACCCCATGATTTCCATCAGCAATACCGGt                                                                     <  1:1750500/52‑1 (MQ=255)
             ggtggCGTATTCACCGCGCTCAAACCCCATGATTTCCATCAGCAATACCGGt                                                                     <  1:2404522/52‑1 (MQ=255)
             ggtggCGTATTCACCGCGCTCAAACCCCATGATTTCCATCAGCAATACCGGt                                                                     <  1:3233352/52‑1 (MQ=255)
             ggtggCGTATTCACCGCGCTCAAACCCCATGATTTCCATCAGCAATACCGGt                                                                     <  1:1557488/52‑1 (MQ=255)
              gtggCGTATTCACCGCGCTCAAACCCCATGATTTCCATCAGCAATACCGGTGACGTGTTGACGAAAGTg                                                   <  1:3228511/69‑1 (MQ=255)
              gtggCGTATTCACCGCGCTCAAACCCCATGATTTCCATCAGCAATACCGGTGACGTGTTGACGAAAGTg                                                   <  1:600268/69‑1 (MQ=255)
              gtggCGTATTCACCGCGCTCAAACCCCATGATTTCCATCAGCAATACCGGTGACGTGTTGACGAAAGTg                                                   <  1:748463/69‑1 (MQ=255)
              gtggCGTATTCACCGCGCTCAAACCCCATGATTTCCATCAGCAATACCGGTGACGTGTTGACGAAAGTg                                                   <  1:1960309/69‑1 (MQ=255)
              gtggCGTATTCACCGCGCTCAAACCCCATGATTTCCATCAGCAATACCGGTGACGTGTTGACGAAAGTg                                                   <  1:3190999/69‑1 (MQ=255)
              gtggCGTATTCACCGCGCTCAAACCCCATGATTTCCATCAGCAATACCGGTGACGTGTTGACGAAAGTg                                                   <  1:2462341/69‑1 (MQ=255)
              gtggCGTATTCACCGCGCTCAAACCCCATGATTTCCATCAGCAATACCGGTGACGTGTTGACGAAAGTg                                                   <  1:1915383/69‑1 (MQ=255)
              gtggCGTATTCACCGCGCTCAAACCCCATGATTTCCATCAGCAATACCGGTGACGTGTTGACGAAAGTg                                                   <  1:1863139/69‑1 (MQ=255)
              gtggCGTATTCACCGCGCTCAAACCCCATGATTTCCATCAGCAATACCGGTGACGTGTTGACGAAAGTg                                                   <  1:1690509/69‑1 (MQ=255)
               tggCGTATTCACCGCGCTCAAACCCCATGATTTCCATCAGCAATACCGGTGACGTGTTGACGAAAGTg                                                   <  1:862877/68‑1 (MQ=255)
                 gCGTATTCACCGCGCTCAAACCCCATGATTTCCATCAGCAATACCGGTGACGTGTTGACGAAAGTGAgg                                                <  1:473788/69‑1 (MQ=255)
                 gCGTATTCACCGCGCTCAAACCCCATGATTTCCATCAGCAATACCGGTGACGTGTTGACGAAAGTGAgg                                                <  1:1313567/69‑1 (MQ=255)
                 gCGTATTCACCGCGCTCAAACCCCATGATTTCCATCAGCAATACCGGTGACGTGTTGACGAAAGTGAgg                                                <  1:2437200/69‑1 (MQ=255)
                 gCGTATTCACCGCGCTCAAACCCCATGATTTCCATCAGCAATACCGGTGACGTGTTGACGAAAGTGAgg                                                <  1:1338316/69‑1 (MQ=255)
                      ttCACCGCGCTCAAACCCCATGATTTCCATCAGCAATACCGGTGACGTGTTg                                                            >  1:1679970/1‑52 (MQ=255)
                      ttCACCGCGCTCAAACCCCATGATTTCCATCAGCAATACCGGTGACGTGTTg                                                            >  1:470366/1‑52 (MQ=255)
                      ttCACCGCGCTCAAACCCCATGATTTCCATCAGCAATACCGGTGACGTGTTg                                                            >  1:247229/1‑52 (MQ=255)
                      ttCACCGCGCTCAAACCCCATGATTTCCATCAGCAATACCGGTGACGTGTTg                                                            >  1:3081156/1‑52 (MQ=255)
                      ttCACCGCGCTCAAACCCCATGATTTCCATCAGCAATACCGGTGACGTGTTg                                                            >  1:146944/1‑52 (MQ=255)
                      ttCACCGCGCTCAAACCCCATGATTTCCATCAGCAATACCGGTGACGTGTTg                                                            >  1:738956/1‑52 (MQ=255)
                      ttCACCGCGCTCAAACCCCATGATTTCCATCAGCAATACCGGTGACGTGTTg                                                            >  1:3100424/1‑52 (MQ=255)
                        cACCGCGCTCAAACCCCATGATTTCCATCAGCAATACCGGTGACGTGTTGACGAAAGTGAgg                                                <  1:3086857/62‑1 (MQ=255)
                        cACCGCGCTCAAACCCCATGATTTCCATCAGCAATACCGGTGACGTGTTGACGAAAGTGAgg                                                <  1:2143932/62‑1 (MQ=255)
                        cACCGCGCTCAAACCCCATGATTTCCATCAGCAATACCGGTGACGTGTTGACGAAAGTGAgg                                                <  1:2114962/62‑1 (MQ=255)
                        cACCGCGCTCAAACCCCATGATTTCCATCAGCAATACCGGTGACGTGTTGACGAAAGTGAgg                                                <  1:3228614/62‑1 (MQ=255)
                        cACCGCGCTCAAACCCCATGATTTCCATCAGCAATACCGGTGACGTGTTGACGAAAGTGAgg                                                <  1:3388549/62‑1 (MQ=255)
                        cACCGCGCTCAAACCCCATGATTTCCATCAGCAATACCGGTGACGTGTTGACGAAAGTGAgg                                                <  1:949479/62‑1 (MQ=255)
                        cACCGCGCTCAAACCCCATGATTTCCATCAGCAATACCGGTGACGTGTTGACGAAAGTGAGGATCAcc                                          >  1:587092/1‑68 (MQ=255)
                          ccGCGCTCAAAACCCATGATTTCCATCAGCAATACTGGCGACGTGTTGACGAAGGTGAGGATCACCGa                                        <  1:291700/68‑1 (MQ=255)
                          ccGCGCTCAAAACCCATGATTTCCATCAGCAATACTGGCGACGTGTTGACGAAGGTGAGGATCACCGa                                        <  1:2806124/68‑1 (MQ=255)
                          ccGCGCTCAAAACCCATGATTTCCATCAGCAATACTGGCGACGTGTTGACGAAGGTGAGGATCACCGa                                        <  1:857700/68‑1 (MQ=255)
                          ccGCGCTCAAAACCCATGATTTCCATCAGCAATACTGGCGACGTGTTGACGAAGGTGAGGATCACCGa                                        <  1:3094456/68‑1 (MQ=255)
                          ccGCGCTCAAAACCCATGATTTCCATCAGCAATACTGGCGACGTGTTGACGAAGGTGAGGATCACCGa                                        <  1:3382354/68‑1 (MQ=255)
                          ccGCGCTCAAAACCCATGATTTCCATCAGCAATACTGGCGACGTGTTGACGAAGGTGAGGATCACCGa                                        <  1:1128461/68‑1 (MQ=255)
                          ccGCGCTCAAAACCCATGATTTCCATCAGCAATACTGGCGACGTGTTGACGAAGGTGAGGATCACCGa                                        <  1:486938/68‑1 (MQ=255)
                          ccGCGCTCAAAACCCATGATTTCCATCAGCAATACTGGCGACGTGTTGACGAAGGTGAGGATCACCGa                                        <  1:687953/68‑1 (MQ=255)
                          ccGCGCTCAAAACCCATGATTTCCATCAGCAATACTGGCGACGTGTTGACGAAGGTGAGGATCACCGa                                        <  1:55474/68‑1 (MQ=255)
                          ccGCGCTCAAAACCCATGATTTCCATCAGCAATACTGGCGACGTGTTGACGAAGGTGAGGATCACCGa                                        <  1:598624/68‑1 (MQ=255)
                          ccGCGCTCAAAACCCATGATTTCCATCAGCAATACTGGCGACGTGTTGACGAAGGTGAGGATCACCGa                                        <  1:643789/68‑1 (MQ=255)
                          ccGCGCTCAAAACCCATGATTTCCATCAGCAATACTGGCGACGTGTTGACGAAGGTGAGGATCACCGa                                        <  1:2740871/68‑1 (MQ=255)
                          ccGCGCTCAAAACCCATGATTTCCATCAGCAATACTGGCGACGTGTTGACGAAGGTGAGGATCACCGa                                        <  1:1700754/68‑1 (MQ=255)
                          ccGCGCTCAAAACCCATGATTTCCATCAGCAATACTGGCGACGTGTTGACGAAGGTGAGGATCACCGa                                        <  1:2378098/68‑1 (MQ=255)
                          ccGCGCTCAAAACCCATGATTTCCATCAGCAATACTGGCGACGTGTTGACGAAGGTGAGGATCACCGa                                        <  1:1380101/68‑1 (MQ=255)
                          ccGCGCTCAAAACCCATGATTTCCATCAGCAATACTGGCGACGTGTTGACGAAGGTGAGGATCACCGa                                        <  1:2548953/68‑1 (MQ=255)
                          ccGCGCTCAAAACCCATGATTTCCATCAGCAATACTGGCGACGTGTTGACGAAGGTGAGGATCACCGa                                        <  1:1378847/68‑1 (MQ=255)
                          ccGCGCTCAAAACCCATGATTTCCATCAGCAATACTGGCGACGTGTTGACGAAGGTGAGGATCACCGa                                        <  1:263152/68‑1 (MQ=255)
                          ccGCGCTCAAAACCCATGATTTCCATCAGCAATACTGGCGACGTGTTGACGAAGGTGAGGATCACCGa                                        <  1:265459/68‑1 (MQ=255)
                           cgcgCTCAAAACCCATGATTTCCATCAGCAATACTGGCGACGTGTTGACGAAGGTGAGGATCACCGa                                        <  1:743279/67‑1 (MQ=255)
                           cgcgCTCAAAACCCATGATTTCCATCAGCAATACTGGCGACGTGTTGACGAAGGTGAGGATCACCGa                                        <  1:1461750/67‑1 (MQ=255)
                           cgcgCTCAAAACCCATGATTTCCATCAGCAATACTGGCGACGTGGTGACGAAGGTGAGGATCACCGa                                        <  1:2031473/67‑1 (MQ=255)
                                           gATTTCCATCAGCAATACCGGTGACGTGTTGACGAAAGTGAGGATCACCGAAACGCTGAGGGTGGTGAt                      >  1:800277/1‑69 (MQ=255)
                                            aTTTCCATCAGCAATACTGGCGACGTGTTGACGAAGGTGAGGATCACCGa                                        <  1:1198781/50‑1 (MQ=255)
                                              ttCCATCAGCAATACCGGTGACGTGTTGACGAAAGTGAGGATCACCGAAACGCTGAGGGTGGTGATaac                   <  1:511183/69‑1 (MQ=255)
                                                ccATCAGCAATACTGGCGACGTGTTGACGAAGGTGAGGATCACCGAAACGCTGAGGGTGGTGATaacaa                 >  1:1350549/1‑69 (MQ=255)
                                                ccATCAGCAATACTGGCGACGTGTTGACGAAGGTGAGGATCACCGAAACGCTGAGGGTGGTGATaacaa                 >  1:277464/1‑69 (MQ=255)
                                                ccATCAGCAATACTGGCGACGTGTTGACGAAGGTGAGGATCACCGAAACGCTGAGGGTGGTGATaacaa                 >  1:978401/1‑69 (MQ=255)
                                                ccATCAGCAATACTGGCGACGTGTTGACGAAGGTGAGGATCACCGAAACGCTGAGGGTGGTGATaacaa                 >  1:3421305/1‑69 (MQ=255)
                                                ccATCAGCAATACTGGCGACGTGTTGACGAAGGTGAGGATCACCGAAACGCTGAGGGTGGTGATaacaa                 >  1:3288348/1‑69 (MQ=255)
                                                ccATCAGCAATACTGGCGAAGTGTTGACGAAGGTGAGGATCACCGaa                                       >  1:3296321/1‑47 (MQ=255)
                                                 cATCAGCAATACTGGCGACGTGTTGACGAAGGTGAGGATCACCGAAACGCTGAGGGTGGTGATaacaa                 <  1:322371/68‑1 (MQ=255)
                                                 cATCAGCAATACTGGCGACGTGTTGACGAAGGTGAGGATCACCGAAACGCTGAGGGTGGTGATaacaa                 <  1:2336841/68‑1 (MQ=255)
                                                 cATCAGCAATACTGGCGACGTGTTGACGAAGGTGAGGATCACCGAAACGCTGAGGGTGGTGATaacaa                 <  1:1595561/68‑1 (MQ=255)
                                                 cATCAGCAATACTGGCGACGTGTTGACGAAGGTGAGGATCACCGAAACGCTGAGGGTGGTGATaacaa                 <  1:765972/68‑1 (MQ=255)
                                                 cATCAGCAATACTGGCGACGTGTTGACGAAGGTGAGGATCACCGAAACGCTGAGGGTGGTGATaacaa                 <  1:1719173/68‑1 (MQ=255)
                                                 cATCAGCAATACTGGCGACGTGTTGACGAAGGTGAGGATCACCGAAACGCTGAGGGTGGTGATaacaa                 <  1:81172/68‑1 (MQ=255)
                                                 cATCAGCAATACTGGCGACGTGTTGACGAAGGTGAGGATCACCGAAACGCTGAGGGTGGTGATaacaa                 <  1:117549/68‑1 (MQ=255)
                                                 cATCAGCAATACTGGCGACGTGTTGACGAAGGTGAGGATCACCGAAACGCTGAGGGTGGTGATaacaa                 <  1:1156413/68‑1 (MQ=255)
                                                 cATCAGCAATACTGGCGACGTGTTGACGAAGGTGAGGATCACCGAAACGCTGAGGGTGGTGATaacaa                 <  1:1919110/68‑1 (MQ=255)
                                                 cATCAGCAATACTGGCGACGTGTTGACGAAGGTGAGGATCACCGAAACGCTGAGGGTGGTGATaacaa                 <  1:3338045/68‑1 (MQ=255)
                                                 cATCAGCAATACTGGCGACGTGTTGACGAAGGTGAGGATCACCGAAACGCTGAGGGTGGTGATaacaa                 <  1:204735/68‑1 (MQ=255)
                                                 cATCAGCAATACTGGCGACGTGTTGACGAAGGTGAGGATCACCGAAACGCTGAGGGTGGTGATaacaa                 <  1:3280749/68‑1 (MQ=255)
                                                 cATCAGCAATACTGGCGACGTGTTGACGAAGGTGAGGATCACCGAAACGCTGAGGGTGGTGATaacaa                 <  1:1923694/68‑1 (MQ=255)
                                                 cATCAGCAATACTGGCGACGTGTTGACGAAGGTGAGCATCACCGAAACGCTGAGGGTGGTGATaacaa                 <  1:2932546/68‑1 (MQ=255)
                                                 cATCAGCAATACCGGTGACGTGTTGACGAAAGTGAGGATCACCGAAACGCTGAGGGTGGTGATaacaa                 <  1:2849904/68‑1 (MQ=255)
                                                 cATCAGCAATACCGGTGACGTGTTGACGAAAGTGAGGATCACCGAAACGCTGAGGGTGGTGATaacaa                 <  1:3083725/68‑1 (MQ=255)
                                                        aaTACCGGTGACGTGTTGACGAAAGTGAGGATCACCGAAACGCTGAGGGTGGTGATAACAACACGGCTg         >  1:3006054/1‑69 (MQ=255)
                                                        aaTACCGGTGACGTGTTGACGAAAGTGAGGATCACCGAAACGCTGAGGGTGGTGATAACAACACGGCTg         >  1:1270520/1‑69 (MQ=255)
                                                        aaTACCGGTGACGTGTTGACGAAAGTGAGGATCACCGAAACGCTGAGGGTGGTGATAACAACACGGCTg         >  1:2246377/1‑69 (MQ=255)
                                                        aaTACCGGTGACGTGTTGACGAAAGTGAGGATCACCGAAACGCTGAGGGTGGTGATAACAACACGGCTg         >  1:217861/1‑69 (MQ=255)
                                                         aTACTGGCGACGTGTTGACGAAGGTGAGGATCACCGa                                        <  1:1817353/37‑1 (MQ=25)
                                                            ccGGTGACGTGTTGACGAAAGTGAGGATCACCGAAACGCTGAGGGTGGTGATAACAACACGGCTGAgg      >  1:3095023/1‑68 (MQ=255)
                                                            ccGGTGACGTGTTGACGAAAGTGAGGATCACCGAAACGCTGAGGGTGGTGATAACAACACGGCTGAgg      >  1:1289407/1‑68 (MQ=255)
                                                            ccGGTGACGTGTTGACGAAAGTGAGGATCACCGAAACGCTGAGGGTGGTGATAACAACACGGCTGAgg      >  1:2931141/1‑68 (MQ=255)
                                                            ccGGTGACGTGTTGACGAAAGTGAGGATCACCGAAACGCTGAGGGTGGTGATAACAACACGGCTGAgg      >  1:2930369/1‑68 (MQ=255)
                                                            ccGGTGACGTGTTGACGAAAGTGAGGATCACCGAAACGCTGAGGGTGGTGATAACAACACGGCTGAgg      >  1:2903043/1‑68 (MQ=255)
                                                            ccGGTGACGTGTTGACGAAAGTGAGGATCACCGAAACGCTGAGGGTGGTGATAACAACACGGCTGAgg      >  1:3168240/1‑68 (MQ=255)
                                                            ccGGTGACGTGTTGACGAAAGTGAGGATCACCGAAACGCTGAGGGTGGTGATAACAACACGGCTGAgg      >  1:1175759/1‑68 (MQ=255)
                                                            ccGGTGACGTGTTGACGAAAGTGAGGATCACCGAAACGCTGAGGGTGGTGATAACAACACGGCTGAg       >  1:1431849/1‑67 (MQ=255)
                                                            ccGATGACGTGTTGACGAAAGTGAGGATCACCGAAACGCTGAGGGTGGTGATAACAACACGGCTGAgg      >  1:3414252/1‑68 (MQ=255)
                                                               gTGACGTGTTGACGAAAGTGAGGATCACCGAAACGCTGAGGGTGGTGATAACAACACGGCTGAGGaaaa  <  1:751565/69‑1 (MQ=255)
                                                                |                                                                   
TCAGCGCCATAATGGTGGCGTATTCACCGCGCTCAAACCCCATGATTTCCATCAGCAATACCGGTGACGTGTTGACGAAAGTGAGGATCACCGAAACGCTGAGGGTGGTGATAACAACACGGCTGAGGAAAA  >  minE/2482125‑2482256

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