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 615,056 C→T 45.5% G235G (GGC→GGT) ‡ serC → 3‑phosphoserine/phosphohydroxythreonine aminotransferase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE615,0560CT45.5% 26.2 / 101.6 123G235G (GGC→GGT) ‡serC3‑phosphoserine/phosphohydroxythreonine aminotransferase
Reads supporting (aligned to +/- strand):  ref base C (30/37);  new base T (28/28);  total (58/65)
Fisher's exact test for biased strand distribution p-value = 5.91e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.47e-01

Only 100 of 124 total aligned reads displayed.

TGCTGGGCAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGACATTTGCCTGGTATCTATCTGGTCTGGTCTTTA  >  minE/614992‑615111
                                                                |                                                       
tGCTGGGCAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCa                                                     >  1:2973246/1‑69 (MQ=255)
tGCTGGGCAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCa                                                     >  1:1826383/1‑69 (MQ=255)
tGCTGGGCAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCa                                                     >  1:1016786/1‑69 (MQ=255)
   tGGGCAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATg                                                   <  1:2012771/68‑1 (MQ=255)
   tGGGCAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATg                                                   <  1:1704575/68‑1 (MQ=255)
   tGGGCAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATg                                                   <  1:2495653/68‑1 (MQ=255)
       cAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGttt                                                <  1:2136304/67‑1 (MQ=255)
       cAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGttt                                                <  1:3315192/67‑1 (MQ=255)
       cAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGttt                                                <  1:1436857/67‑1 (MQ=255)
       cAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGttt                                                <  1:2266509/67‑1 (MQ=255)
       cAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTaa                                              <  1:2801997/69‑1 (MQ=255)
       cAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTaa                                              <  1:3391691/69‑1 (MQ=255)
       cAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTaa                                              <  1:3224386/69‑1 (MQ=255)
       cAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTaa                                              <  1:2008863/69‑1 (MQ=255)
       cAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTaa                                              <  1:599385/69‑1 (MQ=255)
       cAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTaa                                              <  1:3074302/69‑1 (MQ=255)
       cAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTaa                                              <  1:1128620/69‑1 (MQ=255)
       cAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTaa                                              <  1:2531606/69‑1 (MQ=255)
       cAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTaa                                              <  1:77056/69‑1 (MQ=255)
        aaaGCGAATATCGCCTGCCCATCGATTCTGGATTACTCCATCCTCAACGATAACGATTCCAt                                                    <  1:1531487/62‑1 (MQ=255)
        aaaGCGAATATCGCCTGCCCATCGATTCTGGATTACTCCATCCTCAACGATAACGATTCCAt                                                    <  1:2042774/62‑1 (MQ=255)
        aaaGCGAATATCGCCTGCCCATCGATTCTGGATTACTCCATCCTCAACGATAACGATTCCAt                                                    <  1:272270/62‑1 (MQ=255)
        aaaGCGAATATCGCCTGCCCATCGATTCTGGATTACTCCATCCTCAACGATAACGATTCCAt                                                    <  1:157780/62‑1 (MQ=255)
        aaaGCGAATATCGCCTGCCCATCGATTCTGGATTACTCCATCCTCAACGATAACGATTCCAt                                                    <  1:1929735/62‑1 (MQ=255)
        aaaGCGAATATCGCCTGCCCATCGATTCTGGATTACTCCATCCTCAACGATAACGATTCCAt                                                    <  1:2251158/62‑1 (MQ=255)
        aaaGCGAATATCGCCTGCCCATCGATTCTGGATTACTCCATCCTCAACGATAACGATTCCAt                                                    <  1:2770392/62‑1 (MQ=255)
        aaaGCGAATATCGCCTGCCCATCGATTCTGGATTACTCCATCCTCAACGATAACGATTCCAt                                                    <  1:1804135/62‑1 (MQ=255)
        aaaGCGAATATCGCCTGCCCATCGATTCTGGATTACTCCATCCTCAACGATAACGATTCCAt                                                    <  1:2283802/62‑1 (MQ=255)
        aaaGCGAATATCGCCTGCCCATCGATTCTGGATTACTCCATCCTCAACGATAACGATTCCAt                                                    <  1:698796/62‑1 (MQ=255)
        aaaGCGAATATCGCCTGCCCATCGATTCTGGATTACTCCATCCTCAACGATAACGATTCCAt                                                    <  1:1738739/62‑1 (MQ=255)
         aaGCGAATATCGCCTGCCCATCGATTCTGGATTACTCCATCCTCAACGATAACGATTCCAt                                                    <  1:548238/61‑1 (MQ=255)
          aGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAacac                                           <  1:863835/69‑1 (MQ=255)
              aaTATCGGCTGGCCATCGATTCTGGATTACTCCATCCTCAACGATAACGATTCCAt                                                    <  1:2132655/56‑1 (MQ=255)
                  tCGCGTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGa                                   >  1:2381103/1‑69 (MQ=255)
                  tCGCGTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCAGCCGa                                   >  1:1963873/1‑69 (MQ=255)
                    gcgTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGCCa                                 <  1:1461563/69‑1 (MQ=255)
                    gcgTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGACa                                 <  1:3186298/69‑1 (MQ=255)
                    gcgTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGACa                                 <  1:2974625/69‑1 (MQ=255)
                    gcgTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGACa                                 <  1:261932/69‑1 (MQ=255)
                    gcgTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGACa                                 <  1:975698/69‑1 (MQ=255)
                    gcgTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGACa                                 <  1:1901405/69‑1 (MQ=255)
                    gcgTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGACa                                 <  1:615599/69‑1 (MQ=255)
                    gcgTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGACa                                 <  1:1227620/69‑1 (MQ=255)
                    gcgTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGACa                                 <  1:145142/69‑1 (MQ=255)
                    gcgTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGACa                                 <  1:69972/69‑1 (MQ=255)
                          ccGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGACATTTGcc                           >  1:3381704/1‑69 (MQ=255)
                          ccGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGACATTTGcc                           >  1:1802825/1‑69 (MQ=255)
                          ccGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGACATTTGcc                           >  1:2443991/1‑69 (MQ=255)
                          ccGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGACATTTGcc                           >  1:755896/1‑69 (MQ=255)
                          ccGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGACATTTGcc                           >  1:1552367/1‑69 (MQ=255)
                           cGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGACATTTGCCt                          <  1:1057227/69‑1 (MQ=255)
                            atCGATTCTGGATTACTCCATCCTCAACGATAACGATTCCAt                                                    <  1:412323/41‑1 (MQ=255)
                               gATTCTGGATTACTCCATCCTTAACGATAACGATTCCATGTTCAac                                             >  1:2997454/1‑46 (MQ=25)
                               gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCaa                                              >  1:761690/1‑45 (MQ=255)
                               gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                                             >  1:3022708/1‑46 (MQ=255)
                               gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                                             >  1:693954/1‑46 (MQ=255)
                               gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                                             >  1:953750/1‑46 (MQ=255)
                               gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                                             >  1:316965/1‑46 (MQ=255)
                               gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                                             >  1:967627/1‑46 (MQ=255)
                               gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                                             >  1:597674/1‑46 (MQ=255)
                               gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                                             >  1:2483330/1‑46 (MQ=255)
                               gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                                             >  1:2962818/1‑46 (MQ=255)
                               gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                                             >  1:2202095/1‑46 (MQ=255)
                               gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                                             >  1:2926321/1‑46 (MQ=255)
                               gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                                             >  1:1890171/1‑46 (MQ=255)
                               gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                                             >  1:2082691/1‑46 (MQ=255)
                               gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                                             >  1:1749551/1‑46 (MQ=255)
                               gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                                             >  1:2159136/1‑46 (MQ=255)
                               gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                                             >  1:217016/1‑46 (MQ=255)
                               gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                                             >  1:2351231/1‑46 (MQ=255)
                               gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                                             >  1:2412733/1‑46 (MQ=255)
                               gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                                             >  1:1399831/1‑46 (MQ=255)
                               gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                                             >  1:2530137/1‑46 (MQ=255)
                               gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                                             >  1:1389405/1‑46 (MQ=255)
                               gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                                             >  1:1269048/1‑46 (MQ=255)
                               gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                                             >  1:1088381/1‑46 (MQ=255)
                               gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                                             >  1:2812168/1‑46 (MQ=255)
                                   cTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGAc                                  >  1:495457/1‑53 (MQ=255)
                                   cTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGAc                                  >  1:757916/1‑53 (MQ=255)
                                   cTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGAc                                  >  1:642930/1‑53 (MQ=255)
                                   cTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGAc                                  >  1:1986862/1‑53 (MQ=255)
                                   cTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGAc                                  >  1:1032027/1‑53 (MQ=255)
                                   cTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGAc                                  >  1:47696/1‑53 (MQ=255)
                                   cTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGAc                                  >  1:3064436/1‑53 (MQ=255)
                                     ggATTATTCCATCCTCAACGATAACGTCTCCATGttt                                                <  1:2047288/37‑1 (MQ=255)
                                             ccATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGACATTTGCCTGGTATCTAtctggtctgg        >  1:581050/1‑69 (MQ=255)
                                             ccATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGACATTTGCCTGGTATCTAtctggtctgg        >  1:1784204/1‑69 (MQ=255)
                                             ccATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGACATTTGCCTGGTATCTAtctggtctgg        >  1:3372302/1‑69 (MQ=255)
                                             ccATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGACATTTGCCTGGTATCTAtctggtctgg        >  1:2079359/1‑69 (MQ=255)
                                             ccATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGACATTTGCCTGGTATCTAtctggtctgg        >  1:1621876/1‑69 (MQ=255)
                                             ccATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGACATTTGCCTGGTATCTAtctggtctgg        >  1:3232092/1‑69 (MQ=255)
                                             ccATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGACATTTGCCTGGTATCTAtctggtctgg        >  1:1470328/1‑69 (MQ=255)
                                                tCCTCAACGATAACGATTCCATGTTCAACACGCCGCCGACATTTGCCTGGTACTTATctggcctggt       <  1:169106/67‑1 (MQ=255)
                                                tCCTCAACGATAACGATTCCATGTTCAACACGCCGCCGACATTTGCCTGGTACTTATctggcctggt       <  1:272242/67‑1 (MQ=255)
                                                tCCTCAACGATAACGATTCCATGTTCAACACGCCGCCGACATTTGCCTGGTACTTATctggcctggt       <  1:268536/67‑1 (MQ=255)
                                                tCCTCAACGATAACGATTCCATGTTCAACACGCCGCCGACATTTGCCTGGTACTTATctggcctggt       <  1:2652213/67‑1 (MQ=255)
                                                tCCTCAACGATAACGATTCCATGTTCAACACGCCGCCGACATTTGCCTGGTACTTATctggcctggt       <  1:2080678/67‑1 (MQ=255)
                                                tCCTCAACGATAACGATTCCATGTTCAACACGCCGCCGACATTTGCCTGGTACTTATctggcctggt       <  1:601711/67‑1 (MQ=255)
                                                 ccTCAACGATAACGATTCCATGTTCAACACGCCGCCGACATTTGCCTGGTACTTATctggcctggt       <  1:2123783/66‑1 (MQ=255)
                                                                cTCCATGTTTAACACGCCGCCGACATTTGCCTGGTATCTATCTGGTCTGGTCTTTa  <  1:2952560/56‑1 (MQ=255)
                                                                |                                                       
TGCTGGGCAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGACATTTGCCTGGTATCTATCTGGTCTGGTCTTTA  >  minE/614992‑615111

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