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 429,633 G→T 60.6% E80D (GAG→GAT)  glnS → glutamyl‑tRNA synthetase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE429,6330GT60.6% 53.4 / 130.8 132E80D (GAG→GAT) glnSglutamyl‑tRNA synthetase
Reads supporting (aligned to +/- strand):  ref base G (32/20);  new base T (23/57);  total (55/77)
Fisher's exact test for biased strand distribution p-value = 2.75e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.54e-01

Only 100 of 132 total aligned reads displayed.

AAGGCCAGTGCAACCTGCGTTTCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTTGAGTCGATCAAAAACGACGTAGAGTGGTTAGGTTTTCACTGGTCTGGTAACGTCCGTTACTCCTCCG  >  minE/429569‑429697
                                                                |                                                                
aaGGCCAGTGCAACCTGCGTTTCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTTGAGTCg                                                               >  1:1423452/1‑68 (MQ=255)
         gCAACCTGCGTTTCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTc                                                                <  1:1081242/58‑1 (MQ=255)
         gCAACCTGCGTTTCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTc                                                                <  1:2505314/58‑1 (MQ=255)
         gCAACCTGCGTTTCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTc                                                                <  1:2952661/58‑1 (MQ=255)
         gCAACCTGCGTTTCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTc                                                                <  1:2959513/58‑1 (MQ=255)
         gCAACCTGCGTTTCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTc                                                                <  1:1533303/58‑1 (MQ=255)
         gCAACCTGCGTTTCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTc                                                                <  1:1175627/58‑1 (MQ=255)
         gCAACCTGCGTTTCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTc                                                                <  1:606901/58‑1 (MQ=255)
          cAACCTGCGTTTCTACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTc                                                                <  1:2871440/57‑1 (MQ=255)
          cAACCTGCGTTTCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTTGAGTCGATCAAAAacga                                                    >  1:476816/1‑69 (MQ=255)
          cAACCTGCGTTTCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTTGAGTCGATCAAAAacga                                                    >  1:1701486/1‑69 (MQ=255)
          cAACCTGCGTTTCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTTGAGTCGATCAAAAacga                                                    >  1:1490143/1‑69 (MQ=255)
          cAACCTGCGTTTCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTTGAGTCGATCAAAAacga                                                    >  1:3274763/1‑69 (MQ=255)
          cAACCTGCGTTTCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTc                                                                <  1:3287432/57‑1 (MQ=255)
             ccTGCGTTTCTACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTc                                                                <  1:3250966/54‑1 (MQ=255)
              cTGCGTTTCGACGACACTAACCCTGTAAAAGAAGATATCGAGTATGTTGAGTCGATCAAAAACGACGTa                                                <  1:2451604/69‑1 (MQ=255)
              cTGCGTTTCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTTGAGTCGATCAAAAACGACGTa                                                <  1:1333051/69‑1 (MQ=255)
               tGCGTTTCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCa                                                           <  1:2051515/57‑1 (MQ=255)
               tGCGTTTCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCa                                                           <  1:2185188/57‑1 (MQ=255)
               tGCGTTTCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCa                                                           <  1:2254246/57‑1 (MQ=255)
               tGCGTTTCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCa                                                           <  1:1918124/57‑1 (MQ=255)
               tGCGTTTCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCa                                                           <  1:2292117/57‑1 (MQ=255)
               tGCGTTTCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCa                                                           <  1:2362265/57‑1 (MQ=255)
               tGCGTTTCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCa                                                           <  1:2727107/57‑1 (MQ=255)
               tGCGTTTCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCa                                                           <  1:516277/57‑1 (MQ=255)
               tGCGTTTCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCa                                                           <  1:1699761/57‑1 (MQ=255)
               tGCGTTTCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCa                                                           <  1:2902661/57‑1 (MQ=255)
               tGCGTTTCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCa                                                           <  1:890895/57‑1 (MQ=255)
               tGCGTTTCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCa                                                           <  1:86172/57‑1 (MQ=255)
               tGCGTTTCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCa                                                           <  1:3035901/57‑1 (MQ=255)
                gCGTTTCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCa                                                           <  1:1916836/56‑1 (MQ=255)
                  gTTTCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCa                                                           <  1:2592958/54‑1 (MQ=255)
                     tCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTTGAGTCGATCAAAAACGACGTag                                               <  1:2453380/63‑1 (MQ=255)
                     tCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTTGAGTCGATCAAAAACGACGTag                                               <  1:406878/63‑1 (MQ=255)
                     tCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTTGAGTCGATCAAAAACGACGTag                                               <  1:1989819/63‑1 (MQ=255)
                     tCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTTGAGTCGATCAAAAACGACGTag                                               <  1:2258225/63‑1 (MQ=255)
                     tCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTTGAGTCGATCAAAAACGACGTag                                               <  1:381581/63‑1 (MQ=255)
                     tCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTTGAGTCGATCAAAAACGACGTag                                               <  1:2421401/63‑1 (MQ=255)
                     tCGACGACACTAACCCGGTAAAAGAAGATATCGAGTATGTTGAGTCGATCAAAAACGACGTag                                               <  1:2851757/63‑1 (MQ=255)
                      cgacgaCACTAACCCGGTAAAAGAAGATATCGAGTATTTTGAGTCGATCAAAAACGACGTag                                               <  1:698465/62‑1 (MQ=255)
                        acgacACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCTATCAAAAACGACGTAGAGTGGTTa                                       <  1:2109953/68‑1 (MQ=255)
                        acgacACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCAAAAACGACGTAGAGTGGTTa                                       <  1:2877920/68‑1 (MQ=255)
                        acgacACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCAAAAACGACGTAGAGTGGTTa                                       <  1:646758/68‑1 (MQ=255)
                        acgacACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCAAAAACGACGTAGAGTGGTTa                                       <  1:3074838/68‑1 (MQ=255)
                        acgacACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCAAAAACGACGTAGAGTGGTTa                                       <  1:2801507/68‑1 (MQ=255)
                        acgacACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCAAAAACGACGTAGAGTGGTTa                                       <  1:2765233/68‑1 (MQ=255)
                        acgacACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCAAAAACGACGTAGAGTGGTTa                                       <  1:1599/68‑1 (MQ=255)
                        acgacACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCAAAAACGACGTAGAGTGGTTa                                       <  1:5604/68‑1 (MQ=255)
                        acgacACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCAAAAACGACGTAGAGTGGTTa                                       <  1:1339861/68‑1 (MQ=255)
                        acgacACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCAAAAACGACGTAGAGTGGTTa                                       <  1:1482695/68‑1 (MQ=255)
                        acgacACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCAAAAACGACGTAGAGTGGTTa                                       <  1:1880164/68‑1 (MQ=255)
                        acgacACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCAAAAACGACGTAGAGTGGTTa                                       <  1:2362109/68‑1 (MQ=255)
                        acgacACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCAAAAACGACGTAGAGTGGTTa                                       <  1:2398756/68‑1 (MQ=255)
                         cgacACTACCCCGGGAAAAGAAGATATCGAGTATGTCGATTc                                                                <  1:2394650/42‑1 (MQ=255)
                         cgacACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCAAAAACGACGTAGAGTGGTTa                                       <  1:260679/67‑1 (MQ=255)
                         cgacACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCAAAAACGACGTAGAGTGGTTa                                       <  1:1871022/67‑1 (MQ=255)
                         cgacACTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCAAAAACGACGTAGAGTGGTTa                                       <  1:2362830/67‑1 (MQ=255)
                            cacTAACCCGGTAAAAGAAGATATCGAGTATGTCTATTCGATCaaa                                                         >  1:2835076/1‑46 (MQ=255)
                            cacTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCaaa                                                         >  1:3179477/1‑46 (MQ=255)
                            cacTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCaaa                                                         >  1:1239483/1‑46 (MQ=255)
                            cacTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCaaa                                                         >  1:1495892/1‑46 (MQ=255)
                            cacTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCaaa                                                         >  1:3262902/1‑46 (MQ=255)
                            cacTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCaaa                                                         >  1:1315119/1‑46 (MQ=255)
                            cacTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCaaa                                                         >  1:1584261/1‑46 (MQ=255)
                            cacTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCaaa                                                         >  1:2825204/1‑46 (MQ=255)
                            cacTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCaaa                                                         >  1:344624/1‑46 (MQ=255)
                            cacTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCaaa                                                         >  1:466953/1‑46 (MQ=255)
                            cacTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCaaa                                                         >  1:2635051/1‑46 (MQ=255)
                            cacTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCaaa                                                         >  1:92499/1‑46 (MQ=255)
                            cacTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCaaa                                                         >  1:2259133/1‑46 (MQ=255)
                            cacTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCaaa                                                         >  1:2288502/1‑46 (MQ=255)
                            cacTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCaaa                                                         >  1:2321082/1‑46 (MQ=255)
                            cacTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCaaa                                                         >  1:108600/1‑46 (MQ=255)
                            cacTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCaaa                                                         >  1:1103522/1‑46 (MQ=255)
                            cacTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCaaa                                                         >  1:837075/1‑46 (MQ=255)
                            cacTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCaaa                                                         >  1:1599916/1‑46 (MQ=255)
                            cacTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCaaa                                                         >  1:264754/1‑46 (MQ=255)
                            cacTAACCCGGTAAAAGAAGATATCGAGTATGTCGATTCGATCaaa                                                         >  1:820753/1‑46 (MQ=255)
                                accccGGTAAAAGAAGATATCGAGTATGTTGAGTCGATCAAAAACGACGTAGAGTGGTTAGGTTTTCAc                              >  1:2724579/3‑69 (MQ=255)
                                aaCCCGGTAAAAGAAGATATCGAGTATGTTGAGTCGATCAAAAACGACGTAGAGTGGTTAGGTTTTCAc                              >  1:1226526/1‑69 (MQ=255)
                                aaCCCGGTAAAAGAAGATATCGAGTATGTTGAGTCGATCAAAAACGACGTAGAGTGGTTAGGTTTTCAc                              >  1:3015432/1‑69 (MQ=255)
                                aaCCCGGTAAAAGAAGATATCGAGTATGTTGAGTCGATCAAAAACGACGTAGAGTGGTTAGGTTTTCAc                              >  1:678884/1‑69 (MQ=255)
                                aaCCCGGTAAAAGAAGATATCGAGTATGTTGAGTCGATCAAAAACGACGTAGAGTGGTTAGGTTTTCAc                              >  1:906527/1‑69 (MQ=255)
                                aaCCCGGTAAAAGAAGATATCGAGTATGTTGAGTCGATCAAAAACGACGTAGAGTGGTTAGGTTTTCAc                              >  1:621654/1‑69 (MQ=255)
                                aaCCCGGTAAAAGAAGATATCGAGTATGTTGAGTCGATCAAAAACGACGTAGAGTGGTTAGGTTTTCAc                              >  1:3416535/1‑69 (MQ=255)
                                aaCCCGGTAAAAGAAGATATCGAGTATGTTGAGTCGATCAAAAACGACGTAGAGTGGTTAGGTTTTCAc                              >  1:3200756/1‑69 (MQ=255)
                                aaCCCGGTAAAAGAAGATATCGAGTATGTTGAGTCGATCAAAAACGACGTAGAGTGGTTAGGTTTTCAc                              >  1:3022411/1‑69 (MQ=255)
                                aaCCCGGTAAAAGAAGATATCGAGTATGTTGAGTCGATCAAAAACGACGTAGAGTGGTTAGGTTTTCAc                              >  1:1602878/1‑69 (MQ=255)
                                         aaaGAAGATATCGAGTATGTTGAGTCGATCAAAAACGACGTAGAGTGGTTAGGTTTTCActggtctggt                     <  1:3028628/69‑1 (MQ=255)
                                               gaTATCGAGTATGTTGAGTCGATCAAAAACGACGTAGAGTGGTTAGGTTTTCACTGGTCTGGTAACGTc               <  1:2121282/69‑1 (MQ=255)
                                               gaTATCGAGTATGTCGATTCTATCAAAAACGACGTAGAGTGGTTa                                       <  1:3321497/45‑1 (MQ=255)
                                                atatCGATTATTTTGAGTCTATCAAAAACTACGTAGAGTGGTTAGGTTTTCACTGGTCTGGTAACGTc               <  1:1757240/68‑1 (MQ=255)
                                                atatCGAGTATGTTGAGTCGATCAAAAACGACGTAGAGTGGTTAGGTTTTCACTGGTCTGGTAACGTc               <  1:656458/68‑1 (MQ=255)
                                                            ttGAGTCGATCAAAAACGACGTAGAGTGGTTAGGTTTTCACTGGTCTGGTAACGTCCg             >  1:43350/1‑58 (MQ=255)
                                                            ttGAGTCGATCAAAAACGACGTAGAGTGGTTAGGTTTTCACTGGTCTGGTAACGTCCGtt           >  1:1849682/1‑60 (MQ=255)
                                                            ttGAGTCGATCAAAAACGACGTAGAGTGGTTAGGTTTTCACTGGTCTGGTAACGTCCGt            >  1:1668245/1‑59 (MQ=255)
                                                            ttGAGTCGATCAAAAACGACGTAGAGTGGTTAGGTTTTCACTGGTCTGGTAACGTCCGt            >  1:1998606/1‑59 (MQ=255)
                                                            ttGAGTCGATCAAAAACGACGTAGAGTGGTTAGGTTTTCACTGGTCTGGTAACGTCCGTTACTCCTCCg  >  1:3230255/1‑69 (MQ=255)
                                                            ttGAGTCGATCAAAAACGACGTAGAGTGGTTAGGTTTTCACTGGTCTGGTAACGTCCGTTACTCCTCCg  >  1:1023602/1‑69 (MQ=255)
                                                            ttGAGTCGATCAAAAACGACGTAGAGTGGTTAGGTTTTCACTGGTCTGGTAACGTCCGTTACTCCTCCg  >  1:1779941/1‑69 (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