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 615,065 T→C 39.3% F238F (TTT→TTC)  serC → 3‑phosphoserine/phosphohydroxythreonine aminotransferase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE615,0650TC39.3% 39.5 / 61.3 89F238F (TTT→TTC) serC3‑phosphoserine/phosphohydroxythreonine aminotransferase
Reads supporting (aligned to +/- strand):  ref base T (26/28);  new base C (28/7);  total (54/35)
Fisher's exact test for biased strand distribution p-value = 3.67e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGACATTTGCCTGGTATCTATCTGGTCTGGTCTTTA  >  minE/614999‑615111
                                                                  |                                              
cAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGttt                                                <  1:2136304/67‑1 (MQ=255)
cAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGttt                                                <  1:2266509/67‑1 (MQ=255)
cAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGttt                                                <  1:1662265/67‑1 (MQ=255)
cAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGttt                                                <  1:3315192/67‑1 (MQ=255)
cAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGttt                                                <  1:1436857/67‑1 (MQ=255)
cAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTaa                                              <  1:2008863/69‑1 (MQ=255)
cAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTaa                                              <  1:2531606/69‑1 (MQ=255)
cAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTaa                                              <  1:2801997/69‑1 (MQ=255)
cAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTaa                                              <  1:3074302/69‑1 (MQ=255)
cAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTaa                                              <  1:3224386/69‑1 (MQ=255)
cAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTaa                                              <  1:3391691/69‑1 (MQ=255)
cAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTaa                                              <  1:595993/69‑1 (MQ=255)
cAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTaa                                              <  1:599385/69‑1 (MQ=255)
cAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTaa                                              <  1:77056/69‑1 (MQ=255)
cAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTaa                                              <  1:1128620/69‑1 (MQ=255)
   aGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAacac                                           <  1:863835/69‑1 (MQ=255)
   aGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAacac                                           <  1:1185231/69‑1 (MQ=255)
   aGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAacac                                           <  1:272812/69‑1 (MQ=255)
           tCGCGTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGa                                   >  1:2381103/1‑69 (MQ=255)
           tCGCGTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGa                                   >  1:99872/1‑69 (MQ=255)
           tCGCGTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCAGCCGa                                   >  1:1963873/1‑69 (MQ=255)
             gcgTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGCCa                                 <  1:1461563/69‑1 (MQ=255)
             gcgTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGACa                                 <  1:615599/69‑1 (MQ=255)
             gcgTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGACa                                 <  1:69972/69‑1 (MQ=255)
             gcgTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGACa                                 <  1:3186298/69‑1 (MQ=255)
             gcgTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGACa                                 <  1:2974625/69‑1 (MQ=255)
             gcgTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGACa                                 <  1:975698/69‑1 (MQ=255)
             gcgTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGACa                                 <  1:261932/69‑1 (MQ=255)
             gcgTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGACa                                 <  1:1992178/69‑1 (MQ=255)
             gcgTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGACa                                 <  1:1227620/69‑1 (MQ=255)
             gcgTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGACa                                 <  1:153080/69‑1 (MQ=255)
             gcgTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGACa                                 <  1:145142/69‑1 (MQ=255)
             gcgTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGACa                                 <  1:1901405/69‑1 (MQ=255)
                   ccGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGACATTTGcc                           >  1:1802825/1‑69 (MQ=255)
                   ccGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGACATTTGcc                           >  1:3077426/1‑69 (MQ=255)
                   ccGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGACATTTGcc                           >  1:1552367/1‑69 (MQ=255)
                   ccGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGACATTTGcc                           >  1:3381704/1‑69 (MQ=255)
                   ccGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGACATTTGcc                           >  1:755896/1‑69 (MQ=255)
                   ccGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGACATTTGcc                           >  1:2443991/1‑69 (MQ=255)
                    cGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGACATTTGCCt                          <  1:1057227/69‑1 (MQ=255)
                        gATTCTGGATTACTCCATCCTTAACGATAACGATTCCATGTTCAac                                             >  1:2997454/1‑46 (MQ=25)
                        gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCaa                                              >  1:761690/1‑45 (MQ=255)
                        gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                                             >  1:693954/1‑46 (MQ=255)
                        gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                                             >  1:1399831/1‑46 (MQ=255)
                        gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                                             >  1:1389405/1‑46 (MQ=255)
                        gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                                             >  1:71841/1‑46 (MQ=255)
                        gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                                             >  1:597674/1‑46 (MQ=255)
                        gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                                             >  1:1269048/1‑46 (MQ=255)
                        gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                                             >  1:953750/1‑46 (MQ=255)
                        gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                                             >  1:316965/1‑46 (MQ=255)
                        gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                                             >  1:967627/1‑46 (MQ=255)
                        gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                                             >  1:1749551/1‑46 (MQ=255)
                        gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                                             >  1:1088381/1‑46 (MQ=255)
                        gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                                             >  1:3022708/1‑46 (MQ=255)
                        gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                                             >  1:1776450/1‑46 (MQ=255)
                        gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                                             >  1:2962818/1‑46 (MQ=255)
                        gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                                             >  1:2202095/1‑46 (MQ=255)
                        gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                                             >  1:2483330/1‑46 (MQ=255)
                        gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                                             >  1:2412733/1‑46 (MQ=255)
                        gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                                             >  1:2530137/1‑46 (MQ=255)
                        gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                                             >  1:1890171/1‑46 (MQ=255)
                        gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                                             >  1:2351231/1‑46 (MQ=255)
                        gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                                             >  1:217016/1‑46 (MQ=255)
                        gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                                             >  1:2638824/1‑46 (MQ=255)
                        gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                                             >  1:2159136/1‑46 (MQ=255)
                        gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                                             >  1:2082691/1‑46 (MQ=255)
                        gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                                             >  1:2812168/1‑46 (MQ=255)
                        gATTCTGGATTACTCCATCCTCAACGATAACGATTCCATGTTCAac                                             >  1:2926321/1‑46 (MQ=255)
                           tCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGACATTTGCCTGGtatct                   <  1:2066864/69‑1 (MQ=255)
                            cTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGAc                                  >  1:757916/1‑53 (MQ=255)
                            cTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGAc                                  >  1:3064436/1‑53 (MQ=255)
                            cTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGAc                                  >  1:1986862/1‑53 (MQ=255)
                            cTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGAc                                  >  1:1032027/1‑53 (MQ=255)
                            cTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGAc                                  >  1:642930/1‑53 (MQ=255)
                            cTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGAc                                  >  1:47696/1‑53 (MQ=255)
                            cTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGAc                                  >  1:495457/1‑53 (MQ=255)
                            cTGGATTATTCCATCCTCAACGATAACGGCTCAATGTTTAACACGCCGCCGAc                                  >  1:3284511/1‑53 (MQ=255)
                              ggATTATTCCATCCTCAACGATAACGTCTCCATGttt                                                <  1:2047288/37‑1 (MQ=255)
                                      ccATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGACATTTGCCTGGTATCTAtctggtctgg        >  1:581050/1‑69 (MQ=255)
                                      ccATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGACATTTGCCTGGTATCTAtctggtctgg        >  1:2927475/1‑69 (MQ=255)
                                      ccATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGACATTTGCCTGGTATCTAtctggtctgg        >  1:2079359/1‑69 (MQ=255)
                                      ccATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGACATTTGCCTGGTATCTAtctggtctgg        >  1:1784204/1‑69 (MQ=255)
                                      ccATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGACATTTGCCTGGTATCTAtctggtctgg        >  1:1621876/1‑69 (MQ=255)
                                      ccATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGACATTTGCCTGGTATCTAtctggtctgg        >  1:3232092/1‑69 (MQ=255)
                                      ccATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGACATTTGCCTGGTATCTAtctggtctgg        >  1:3372302/1‑69 (MQ=255)
                                      ccATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGACATTTGCCTGGTATCTAtctggtctgg        >  1:1859209/1‑69 (MQ=255)
                                      ccATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGACATTTGCCTGGTATCTAtctggtctgg        >  1:1470328/1‑69 (MQ=255)
                                         tCCTCAACGATAACGATTCCATGTTCAACACGCCGCCGACATTTGCCTGGTACTTATctggcctggt       <  1:169106/67‑1 (MQ=255)
                                         tCCTCAACGATAACGATTCCATGTTCAACACGCCGCCGACATTTGCCTGGTACTTATctggcctggt       <  1:2652213/67‑1 (MQ=255)
                                         tCCTCAACGATAACGATTCCATGTTCAACACGCCGCCGACATTTGCCTGGTACTTATctggcctggt       <  1:268536/67‑1 (MQ=255)
                                         tCCTCAACGATAACGATTCCATGTTCAACACGCCGCCGACATTTGCCTGGTACTTATctggcctggt       <  1:272242/67‑1 (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)
                                                                  |                                              
CAAAGCGAATATCGCGTGTCCGTCGATTCTGGATTATTCCATCCTCAACGATAACGGCTCCATGTTTAACACGCCGCCGACATTTGCCTGGTATCTATCTGGTCTGGTCTTTA  >  minE/614999‑615111

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