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 429,630 T→C 61.6% V79V (GTT→GTC)  glnS → glutamyl‑tRNA synthetase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE429,6300TC61.6% 75.2 / 85.0 130V79V (GTT→GTC) glnSglutamyl‑tRNA synthetase
Reads supporting (aligned to +/- strand):  ref base T (26/24);  new base C (23/57);  total (49/81)
Fisher's exact test for biased strand distribution p-value = 9.53e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.62e-01

Only 100 of 142 total aligned reads displayed.

AAGGCCAGTGCAACCTGCGTTTCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTTGAGTCGATCAAAAACGACGTAGAGTGGTTAGGTTTTCACTGGTCTGGTAACGTCCGTTACTCCTCCG  >  minE/429569‑429697
                                                             |                                                                   
aaGGCCAGTGCAACCTGCGTTTCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTTGAGTCg                                                               >  1:1423452/1‑68 (MQ=255)
         gCAACCTGCGTTTCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTc                                                                <  1:1081242/58‑1 (MQ=255)
         gCAACCTGCGTTTCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTc                                                                <  1:2952661/58‑1 (MQ=255)
         gCAACCTGCGTTTCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTc                                                                <  1:1533303/58‑1 (MQ=255)
         gCAACCTGCGTTTCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTc                                                                <  1:2505314/58‑1 (MQ=255)
          cAACCTGCGTTTCTACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTc                                                                <  1:2871440/57‑1 (MQ=255)
          cAACCTGCGTTTCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTTGAGTCGATCAAAAacga                                                    >  1:1701486/1‑69 (MQ=255)
          cAACCTGCGTTTCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTTGAGTCGATCAAAAacga                                                    >  1:3274763/1‑69 (MQ=255)
          cAACCTGCGTTTCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTTGAGTCGATCAAAAacga                                                    >  1:3180758/1‑69 (MQ=255)
          cAACCTGCGTTTCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTc                                                                <  1:3287432/57‑1 (MQ=255)
            aCCTGCGTTTCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTTg                                                                    >  1:2596234/1‑51 (MQ=255)
            aCCTGCGTTTCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTTg                                                                    >  1:1856981/1‑51 (MQ=255)
            aCCTGCGTTTCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTTg                                                                    >  1:2104688/1‑51 (MQ=255)
            aCCTGCGTTTCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTTg                                                                    <  1:2235906/51‑1 (MQ=255)
            aCCTGCGTTTCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTTg                                                                    >  1:25832/1‑51 (MQ=255)
            aCCTGCGTTTCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTTg                                                                    <  1:1029103/51‑1 (MQ=255)
            aCCTGCGTTTCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTTg                                                                    <  1:2662447/51‑1 (MQ=255)
            aCCTGCGTTTCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTTg                                                                    >  1:837063/1‑51 (MQ=255)
             ccTGCGTTTCTACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTc                                                                <  1:3250966/54‑1 (MQ=255)
              cTGCGTTTCGACGACACTAACCCGGTAAAAGAAGATATCTAGTATGTTGAGTCGATCAAAAACGACGTa                                                <  1:1257525/69‑1 (MQ=255)
              cTGCGTTTCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTTGAGTCGATCAAAAACGACGTa                                                <  1:1333051/69‑1 (MQ=255)
               tGCGTTTCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCa                                                           <  1:1918124/57‑1 (MQ=255)
               tGCGTTTCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCa                                                           <  1:2254246/57‑1 (MQ=255)
               tGCGTTTCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCa                                                           <  1:468551/57‑1 (MQ=255)
               tGCGTTTCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCa                                                           <  1:2292117/57‑1 (MQ=255)
               tGCGTTTCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCa                                                           <  1:516277/57‑1 (MQ=255)
               tGCGTTTCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCa                                                           <  1:2421511/57‑1 (MQ=255)
               tGCGTTTCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCa                                                           <  1:2051515/57‑1 (MQ=255)
               tGCGTTTCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCa                                                           <  1:3358550/57‑1 (MQ=255)
               tGCGTTTCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCa                                                           <  1:2727107/57‑1 (MQ=255)
               tGCGTTTCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCa                                                           <  1:2902661/57‑1 (MQ=255)
               tGCGTTTCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCa                                                           <  1:740189/57‑1 (MQ=255)
               tGCGTTTCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCa                                                           <  1:86172/57‑1 (MQ=255)
               tGCGTTTCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCa                                                           <  1:880369/57‑1 (MQ=255)
               tGCGTTTCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCa                                                           <  1:3035901/57‑1 (MQ=255)
                gCGTTTCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCa                                                           <  1:1594472/56‑1 (MQ=255)
                  gTTTCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTc                                                                <  1:1641450/49‑1 (MQ=255)
                  gTTTCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCa                                                           <  1:2592958/54‑1 (MQ=255)
                     tCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTTGAGTCGATCAAAAACGACGTag                                               <  1:2258225/63‑1 (MQ=255)
                     tCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTTGAGTCGATCAAAAACGACGTag                                               <  1:2878112/63‑1 (MQ=255)
                     tCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTTGAGTCGATCAAAAACGACGTag                                               <  1:2769381/63‑1 (MQ=255)
                     tCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTTGAGTCGATCAAAAACGACGTag                                               <  1:381581/63‑1 (MQ=255)
                     tCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTTGAGTCGATCAAAAACGACGTag                                               <  1:2453380/63‑1 (MQ=255)
                     tCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTTGAGTCGATCAAAAACGACGTag                                               <  1:2421401/63‑1 (MQ=255)
                     tCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTTGAGTCGATCAAAAACGACGTag                                               <  1:406878/63‑1 (MQ=255)
                       gacgacACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCa                                                           <  1:1152928/49‑1 (MQ=255)
                        acgacACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCTATCAAAAACGACGTAGAGTGGTTa                                       <  1:2109953/68‑1 (MQ=255)
                        acgacACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCAAAAACGACGTAGAGTGGTTa                                       <  1:646758/68‑1 (MQ=255)
                        acgacACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCAAAAACGACGTAGAGTGGTTa                                       <  1:1599/68‑1 (MQ=255)
                        acgacACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCAAAAACGACGTAGAGTGGTTa                                       <  1:2877920/68‑1 (MQ=255)
                        acgacACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCAAAAACGACGTAGAGTGGTTa                                       <  1:2801507/68‑1 (MQ=255)
                        acgacACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCAAAAACGACGTAGAGTGGTTa                                       <  1:1880164/68‑1 (MQ=255)
                        acgacACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCAAAAACGACGTAGAGTGGTTa                                       <  1:5604/68‑1 (MQ=255)
                        acgacACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCAAAAACGACGTAGAGTGGTTa                                       <  1:2197424/68‑1 (MQ=255)
                        acgacACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCAAAAACGACGTAGAGTGGTTa                                       <  1:1339861/68‑1 (MQ=255)
                        acgacACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCAAAAACGACGTAGAGTGGTTa                                       <  1:1482695/68‑1 (MQ=255)
                        acgacACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCAAAAACGACGTAGAGTGGTTa                                       <  1:1493891/68‑1 (MQ=255)
                        acgacACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCAAAAACGACGTAGAGTGGTTa                                       <  1:2362109/68‑1 (MQ=255)
                         cgacACTACCCCGGGAAAAGAAGATATCGAGTATGTCGATTc                                                                <  1:2394650/42‑1 (MQ=255)
                         cgacACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCAAAAACGACGTAGAGTGGTTa                                       <  1:1871022/67‑1 (MQ=255)
                         cgacACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCAAAAACGACGTAGAGTGGTTa                                       <  1:2362830/67‑1 (MQ=255)
                           acacTAACCCGGTAAATGAAGATATCGAGTATGTCGATTCGATCAAAAACGACGTAGAGTGGTTa                                       <  1:2358156/65‑1 (MQ=255)
                            cacTAACCCGGTAAAAGAAGATATCGAGTATGTCTATTCGATCaaa                                                         >  1:2835076/1‑46 (MQ=255)
                            cacTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCaaa                                                         >  1:3179477/1‑46 (MQ=255)
                            cacTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCaaa                                                         >  1:820753/1‑46 (MQ=255)
                            cacTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCaaa                                                         >  1:92499/1‑46 (MQ=255)
                            cacTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCaaa                                                         >  1:1103522/1‑46 (MQ=255)
                            cacTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCaaa                                                         >  1:39593/1‑46 (MQ=255)
                            cacTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCaaa                                                         >  1:466953/1‑46 (MQ=255)
                            cacTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCaaa                                                         >  1:1495892/1‑46 (MQ=255)
                            cacTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCaaa                                                         >  1:2259133/1‑46 (MQ=255)
                            cacTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCaaa                                                         >  1:1239483/1‑46 (MQ=255)
                            cacTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCaaa                                                         >  1:2288502/1‑46 (MQ=255)
                            cacTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCaaa                                                         >  1:264754/1‑46 (MQ=255)
                            cacTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCaaa                                                         >  1:2635051/1‑46 (MQ=255)
                             acTAACCCGGTAAAAGAAGATATCGAGTATGTTGAGTCGATCAAAAACGACGTAGAGTGGTTAGGtttt                                 <  1:2844571/69‑1 (MQ=255)
                                accccGGTAAAAGAAGATATCGAGTATGTTGAGTCGATCAAAAACGACGTAGAGTGGTTAGGTTTTCAc                              >  1:2724579/3‑69 (MQ=255)
                                aaCCCGGTAAAAGAAGATATCGAGTATGTTGAGTCGATCAAAAACGACGTAGAGTGGTTAGGTTTTCAc                              >  1:3416535/1‑69 (MQ=255)
                                aaCCCGGTAAAAGAAGATATCGAGTATGTTGAGTCGATCAAAAACGACGTAGAGTGGTTAGGTTTTCAc                              >  1:1985357/1‑69 (MQ=255)
                                aaCCCGGTAAAAGAAGATATCGAGTATGTTGAGTCGATCAAAAACGACGTAGAGTGGTTAGGTTTTCAc                              >  1:621654/1‑69 (MQ=255)
                                aaCCCGGTAAAAGAAGATATCGAGTATGTTGAGTCGATCAAAAACGACGTAGAGTGGTTAGGTTTTCAc                              >  1:678884/1‑69 (MQ=255)
                                aaCCCGGTAAAAGAAGATATCGAGTATGTTGAGTCGATCAAAAACGACGTAGAGTGGTTAGGTTTTCAc                              >  1:2384065/1‑69 (MQ=255)
                                aaCCCGGTAAAAGAAGATATCGAGTATGTTGAGTCGATCAAAAACGACGTAGAGTGGTTAGGTTTTCAc                              >  1:1747118/1‑69 (MQ=255)
                                aaCCCGGTAAAAGAAGATATCGAGTATGTTGAGTCGATCAAAAACGACGTAGAGTGGTTAGGTTTTCAc                              >  1:1602878/1‑69 (MQ=255)
                                aaCCCGGTAAAAGAAGATATCGAGTATGTTGAGTCGATCAAAAACGACGTAGAGTGGTTAGGTTTTCAc                              >  1:1226526/1‑69 (MQ=255)
                                aaCCCGGTAAAAGAAGATATCGAGTATGTTGAGTCGATCAAAAACGACGTAGAGTGGTTAGGTTTTCAc                              >  1:906527/1‑69 (MQ=255)
                                aaCCCGGTAAAAGAAGATATCGAGTATGTTGAGTCGATCAAAAACGACGTAGAGTGGTTAGGTTTTCAc                              >  1:3015432/1‑69 (MQ=255)
                                aaCCCGGTAAAAGAAGATATCGAGTATGTTGAGTCGATCAAAAACGACGTAGAGTGGTTAGGTTTTCAc                              >  1:3022411/1‑69 (MQ=255)
                                               gaTATCGAGTATGTTGAGTCGATCAAAAACGACGTAGAGTGGTTAGGTTTTCACTGGTCTGGTAACGTc               <  1:2121282/69‑1 (MQ=255)
                                                atatCGAGTATGTTGAGTCGATCAAAAACGACGTAGAGTGGTTAGGTTTTCACTGGTCTGGTAACGTc               <  1:656458/68‑1 (MQ=255)
                                                            ttGAGTCGATCAAAAACGACGTAGAGTGGTTAGGTTTTCACTGGTCTGGTAAc                  >  1:3033142/1‑53 (MQ=255)
                                                            ttGAGTCGATCAAAAACGACGTAGAGTGGTTAGGTTTTCACTGGTCTGGTAACGTCCGtt           >  1:1849682/1‑60 (MQ=255)
                                                            ttGAGTCGATCAAAAACGACGTAGAGTGGTTAGGTTTTCACTGGTCTGGTAACGTCCGt            >  1:1998606/1‑59 (MQ=255)
                                                            ttGAGTCGATCAAAAACGACGTAGAGTGGTTAGGTTTTCACTGGTCTGGTAACGTCCGt            >  1:2971056/1‑59 (MQ=255)
                                                            ttGAGTCGATCAAAAACGACGTAGAGTGGTTAGGTTTTCACTGGTCTGGTAACGTCCGt            >  1:1668245/1‑59 (MQ=255)
                                                            ttGAGTCGATCAAAAACGACGTAGAGTGGTTAGGTTTTCACTGGTCTGGTAACGTCCGTTACTCCTCCg  >  1:588515/1‑69 (MQ=255)
                                                            ttGAGTCGATCAAAAACGACGTAGAGTGGTTAGGTTTTCACTGGTCTGGTAACGTCCGTTACTCCTCCg  >  1:1779941/1‑69 (MQ=255)
                                                            ttGAGTCGATCAAAAACGACGTAGAGTGGTTAGGTTTTCACTGGTCTGGTAACGTCCGTTACTCCTCCg  >  1:1023602/1‑69 (MQ=255)
                                                            ttGAGTCGATCAAAAACGACGTAGAGTGGTTAGGTTTTCACTGGTCTGGTAACGTCCGTTACTCCTCCg  >  1:3261508/1‑69 (MQ=255)
                                                            ttGAGTCGATCAAAAACGACGTAGAGTGGTTAGGTTTTCACTGGTCTGGTAACGTCCGTTACTCCTCCg  >  1:3230255/1‑69 (MQ=255)
                                                             |                                                                   
AAGGCCAGTGCAACCTGCGTTTCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTTGAGTCGATCAAAAACGACGTAGAGTGGTTAGGTTTTCACTGGTCTGGTAACGTCCGTTACTCCTCCG  >  minE/429569‑429697

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