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 1,049,623 T→G 33.1% V223V (GTT→GTG)  ydhJ → undecaprenyl pyrophosphate phosphatase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,049,6230TG33.1% 127.7 / 120.4 151V223V (GTT→GTG) ydhJundecaprenyl pyrophosphate phosphatase
Reads supporting (aligned to +/- strand):  ref base T (59/42);  new base G (19/31);  total (78/73)
Fisher's exact test for biased strand distribution p-value = 2.43e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.02e-01

Only 100 of 151 total aligned reads displayed.

TCCGCGAAGGTGCACCAGCACAAATTACCCTCTATAGTGATAACAAAACGTTACAGGGTCACGTTTCCAGTATCGGTCGGGCGATTTATGATCAGAGCGTTGAAAGTGACTCAAGCCTTATTCCGGA  >  minE/1049559‑1049685
                                                                |                                                              
taagcgAAGGTGCACCAGCACAAATTACCCTCTATAGTGATAACAAAACGTTACAGGGTCACGTTTcc                                                             >  1:1416606/4‑68 (MQ=255)
tCCGCGAAGGTGCACCAGCACAAATTACCCTCTATAGTGATAACAAAACGTTACAGGGTCACGTTTcc                                                             >  1:179802/1‑68 (MQ=255)
tCCGCGAAGGTGCACCAGCACAAATTACCCTCTATAGTGATAACAAAACGTTACAGGGTCACGTTTcc                                                             >  1:3212772/1‑68 (MQ=255)
tCCGCGAAGGTGCACCAGCACAAATTACCCTCTATAGTGATAACAAAACGTTACAGGGTCACGTTTcc                                                             >  1:1444513/1‑68 (MQ=255)
tCCGCGAAGGTGCACCAGCACAAATTACCCTCTATAGTGATAACAAAACGTTACAGGGTCACGTTTcc                                                             >  1:359675/1‑68 (MQ=255)
tCCGCGAAGGTGCACCAGCACAAATTACCCTCTATAGTGATAACAAAACGTTACAGGGTCACGTTTcc                                                             >  1:2988609/1‑68 (MQ=255)
tCCGCGAAGGTGCACCAGCACAAATTACCCTCTATAGTGATAACAAAACGTTACAGGGTCACGTTTcc                                                             >  1:390846/1‑68 (MQ=255)
tCCGCGAAGGTGCACCAGCACAAATTACCCTCTATAGTGATAACAAAACGTTACAGGGTCACGTTTcc                                                             >  1:2895543/1‑68 (MQ=255)
tCCGCGAAGGTGCACCAGCACAAATTACCCTCTATAGTGATAACAAAACGTTACAGGGTCACGTTTcc                                                             >  1:2660626/1‑68 (MQ=255)
tCCGCGAAGGTGCACCAGCACAAATTACCCTCTATAGTGATAACAAAACGTTACAGGGTCACGTTTcc                                                             >  1:680217/1‑68 (MQ=255)
tCCGCGAAGGTGCACCAGCACAAATTACCCTCTATAGTGATAACAAAACGTTACAGGGTCACGTTTcc                                                             >  1:761648/1‑68 (MQ=255)
tCCGCGAAGGTGCACCAGCACAAATTACCCTCTATAGTGATAACAAAACGTTACAGGGTCACGTTTcc                                                             >  1:828900/1‑68 (MQ=255)
         gTGCACCAGCACAAATTACCCTCTATAGTGATAACAAAACGTTACAGGGTCACGTGTCCAGTAtcggtc                                                   <  1:2640830/69‑1 (MQ=255)
         gTGCACCAGCACAAATTACCCTCTATAGTGATAACAAAACGTTACAGGGTCACGTGTCCAGTAtcggtc                                                   <  1:766655/69‑1 (MQ=255)
         gTGCACCAGCACAAATTACCCTCTATAGTGATAACAAAACGTTACAGGGTCACGTGTCCAGTAtcggtc                                                   <  1:1617886/69‑1 (MQ=255)
         gTGCACCAGCACAAATTACCCTCTATAGTGATAACAAAACGTTACAGGGTCACGTGTCCAGTAtcggtc                                                   <  1:3100861/69‑1 (MQ=255)
          tGCACCAGCACAAATTACCCTCTATAGTGATAACAAAACGTTACAGGGTCACGTTTCCAGTAtcggtcg                                                  >  1:3291309/1‑69 (MQ=255)
          tGCACCAGCACAAATTACCCTCTATAGTGATAACAAAACGTTACAGGGTCACGTTTCCAGTAtcggtcg                                                  >  1:3056160/1‑69 (MQ=255)
          tGCACCAGCACAAATTACCCTCTATAGTGATAACAAAACGTTACAGGGTCACGTGTCCAGTAtcggtc                                                   <  1:1469403/68‑1 (MQ=255)
           gCACCAGCACAAATTACCCTCTATAGTGATAACAAAACGTTACAGGGTCACGTTTCCAGTAtcggtcgg                                                 >  1:643555/1‑69 (MQ=255)
           gCACCAGCACAAATTACCCTCTATAGTGATAACAAAACGTTACAGGGTCACGTTTCCAGTAtcggtcgg                                                 >  1:3331611/1‑69 (MQ=255)
                aGCACAAATTACCCTCTATAGTGATAACAAAACGTTACAGGGTCACGTTTCCAGTATCGGTCGGGCGa                                             <  1:835954/68‑1 (MQ=255)
                    caAATTACCCTCTATAGTGATATCAAAACGTTACAGGGTCACGTGTCCAGTAtcggtc                                                   <  1:260875/58‑1 (MQ=255)
                          aCCCTCTATAGTGATAACAAAACGTTACAGGGTCACGTTTCCAGTATCGGTCGGGCGATTTATGATc                                    >  1:2139211/1‑67 (MQ=255)
                          aCCCTCTATAGTGATAACAAAACGTTACAGGGTCACGTTTCCAGTATCGGTCGGGCGATTTATGATCag                                  >  1:386567/1‑69 (MQ=255)
                          aCCCTCTATAGTGATAACAAAACGTTACAGGGTCACGTTTCCAGTATCGGTCGGGCGATTTATGATCag                                  >  1:2872779/1‑69 (MQ=255)
                          aCCCTCTATAGTGATAACAAAACGTTACAGGGTCACGTTTCCAGTATCGGTCGGGCGATTTATGATCag                                  >  1:2638943/1‑69 (MQ=255)
                               ctATAGTGATAACAAAACGTTACAGGGTCACGTTTCCAGTATCGGTCGGGCGATTTATGATCAGAGCg                              >  1:2737058/1‑68 (MQ=255)
                                    gTGATAACAAAACGTTACAGGGTCACGTGTCCAGTATCGGTCTGGCGATTTATGATCAGAGCGTTGaaa                        <  1:3197721/69‑1 (MQ=255)
                                    gTGATAACAAAACGTTACAGGGTCACGTGTCCAGTATCGGTCGGGCGATTTATGATCAGAGCGTTGaaa                        <  1:46618/69‑1 (MQ=255)
                                    gTGATAACAAAACGTTACAGGGTCACGTGTCCAGTATCGGTCGGGCGATTTATGATCAGAGCGTTGaaa                        <  1:506033/69‑1 (MQ=255)
                                    gTGATAACAAAACGTTACAGGGTCACGTGTCCAGTATCGGTCGGGCGATTTATGATCAGAGCGTTGaaa                        <  1:537795/69‑1 (MQ=255)
                                    gTGATAACAAAACGTTACAGGGTCACGTGTCCAGTATCGGTCGGGCGATTTATGATCAGAGCGTTGaaa                        <  1:1019984/69‑1 (MQ=255)
                                    gTGATAACAAAACGTTACAGGGTCACGTGTCCAGTATCGGTCGGGCGATTTATGATCAGAGCGTTGaaa                        <  1:1003767/69‑1 (MQ=255)
                                    gTGATAACAAAACGTTACAGGGTCACGTGTCCAGTATCGGTCGGGCGATTTATGATCAGAGCGTTGaaa                        <  1:1235228/69‑1 (MQ=255)
                                     tGATAACAAAACGTTACAGGGTCACGTTTCCAGTATCGGTCGGGCGATTTATGATCAGAGCGTTGaaa                        >  1:327468/1‑68 (MQ=255)
                                     tGATAACAAAACGTTACAGGGTCACGTTTCCAGTATCGGTCGGGCGATTTATGATCAGAGCGTTGaaa                        >  1:2128918/1‑68 (MQ=255)
                                     tGATAACAAAACGTTACAGGGTCACGTTTCCAGTATCGGTCGGGCGATTTATGATCAGAGCGTTGaaa                        >  1:1040058/1‑68 (MQ=255)
                                     tGATAACAAAACGTTACAGGGTCACGTTTCCAGTATCGGTCGGGCGATTTATGATCAGAGCGTTGaaa                        >  1:1653530/1‑68 (MQ=255)
                                     tGATAACAAAACGTTACAGGGTCACGTTTCCAGTATCGGTAGGGCGATTTATGATCAGAGCGTTGaaa                        >  1:2249003/1‑68 (MQ=255)
                                     tGATAACAAAACGTTACAGGGTCACGTGTCCAGTATCGGTCGGGCGATTTATGATCAGAGCGTTGaaa                        <  1:3322922/68‑1 (MQ=255)
                                     tGATAACAAAACGTTACAGGGTCACGTGTCCAGTATCGGTCGGGCGATTTATGATCAGAGCGTTGaaa                        <  1:1160349/68‑1 (MQ=255)
                                       aTAACAAAACGTTACAGGGTCACGTTTCCAGTATCGGTCGGGCGATTTATGATCAGAGCGTTGAAAGTg                     >  1:56634/1‑69 (MQ=255)
                                       aTAACAAAACGTTACAGGGTCACGTTTCCAGTATCGGTCGGGCGATTTATGATCAGAGCGTTGAAAGTg                     >  1:662750/1‑69 (MQ=255)
                                       aTAACAAAACGTTACAGGGTCACGTTTCCAGTATCGGTCGGGCGATTTATGATCAGAGCGTTGAAAGTg                     >  1:689870/1‑69 (MQ=255)
                                       aTAACAAAACGTTAAAGGGTCACGTTTCCAGTATCGGTCGGGCGATTTATGATCAGAGCGTTGAAAGTg                     >  1:545413/1‑69 (MQ=255)
                                         aaCAAAACGTTACAGGGTCACGTTTCCAGTATCGGTCGGGCGATTTATGATCag                                  <  1:2821061/54‑1 (MQ=255)
                                         aaCAAAACGTTACAGGGTCACGTTTCCAGTATCGGTCGGGCGATTTATGATCAGAGCGTTGaa                         <  1:1581221/63‑1 (MQ=255)
                                         aaCAAAACGTTACAGGGTCACGTTTCCAGTATCGGTCGGGCGATTTATGATCAGAGCGTTGaa                         <  1:1576777/63‑1 (MQ=255)
                                         aaCAAAACGTTACAGGGTCACGTTTCCAGTATCGGTCGGGCGATTTATGATCAGAGCGTTGaa                         <  1:1377840/63‑1 (MQ=255)
                                         aaCAAAACGTTACAGGGTCACGTTTCCAGTATCGGTCGGGCGATTTATGATCAGAGCGTTGAAAGTGa                    >  1:567889/1‑68 (MQ=255)
                                         aaCAAAACGTTACAGGGTCACGTTTCCAGTATCGGTCGGGCGATTTATGATCAGAGCGTTGAAAGTGa                    >  1:2832037/1‑68 (MQ=255)
                                         aaCAAAACGTTACAGGGTCACGTTTCCAGTATCGGTCGGGCGATTTATGATCAGAGCGTTGAAAGTGa                    >  1:2421184/1‑68 (MQ=255)
                                         aaCAAAACGTTACAGGGTCACGTTTCCAGTATCGGTCGGGCGATTTATGATCAGAGCGTTGAAAGTGa                    >  1:3152883/1‑68 (MQ=255)
                                          aCAAAACGTTACAGGGTCACGTTTCCAGTATCGGTCGGGCGATTTATGATCAGAGCGTTGAAAGTGa                    >  1:2075062/1‑67 (MQ=255)
                                          aCAAAACGTTACAGGGTCACGTTTCCAGTATCGGTCGGGCGATTTATGATCAGAGCGTTGAAAGTGAc                   >  1:1164257/1‑68 (MQ=255)
                                          aCAAAACGTTACAGGGTCACGTTTCCAGTATCGGTCGGGCGATTTATGATCAGAGCGTTGAAAGTGAc                   >  1:1350167/1‑68 (MQ=255)
                                          aCAAAACGTTACAGGGTCACGTTTCCAGTATCGGTCGGGCGATTTATGATCAGAGCGTTGAAAGTGAc                   >  1:1328532/1‑68 (MQ=255)
                                               aCGTTACAGGGTCACGTTTCCAGTATCGGTCGGGCGATTTATGATCAGAGCGTTGAAAGTGACTCAAGc             <  1:260490/69‑1 (MQ=255)
                                                 gTTACAGGGTCACGTTTCCAGTATCGGTCGGGCGATTTATGATCAGAGCGTTGAAAGTGACTCAAGCCt           <  1:2355036/69‑1 (MQ=255)
                                                 gTTACAGGGTCACGTTTCCAGTATCGGTCGGGCGATTTATGATCAGAGCGTTGAAAGTGACTCAAGCCt           <  1:1973171/69‑1 (MQ=255)
                                                 gTTACAGGGTCACGTTTCCAGTATCGGTCGGGCGATTTATGATCAGAGCGTTGAAAGTGACTCAAGCCt           <  1:3359259/69‑1 (MQ=255)
                                                 gTTACAGGGTCACGTTTCCAGTATCGGTCGGGCGATTTATGATCAGAGCGTTGAAAGTGACTCAAGCCt           <  1:3260109/69‑1 (MQ=255)
                                                 gTTACAGGGTCACGTTTCCAGTATCGGTCGGGCGATTTATGATCAGAGCGTTGAAAGTGACTCAAGCCt           <  1:15239/69‑1 (MQ=255)
                                                 gTTACAGGGTCACGTTTCCAGTATCGGTCGGGCGATTTATGATCAGAGCGTTGAAAGTGACTCAAGCCt           <  1:803241/69‑1 (MQ=255)
                                                 gTTACAGGGTCACGTTTCCAGTATCGGTCGGGCGATTTATGATCAGAGCGTTGAAAGTGACTCAAGCCt           <  1:1677988/69‑1 (MQ=255)
                                                 gTTACAGGGTCACGTTTCCAGTATCGGTCGGGCGATTTATGATCAGAGCGTTGAAAGTGACTCAAGCCt           <  1:1290364/69‑1 (MQ=255)
                                                 gTTACAGGGTCACGTTTCCAGTATCGGTCGGGCGATTTATGATCAGAGCGTTGAAAGTGACTCAAGCCt           <  1:1080664/69‑1 (MQ=255)
                                                 gTTACAGGGTCACGTTTCCAGTATCGGTCGGGCGATTTATGATCAGAGCGTTGAAAGTGACTCAAGCCt           <  1:2883398/69‑1 (MQ=255)
                                                 gTTACAGGGTCACGTTTCCAGTATCGGTCGGGCGATTTATGATCAGAGCGTTGAAAGTGACTCAAGCCt           <  1:669610/69‑1 (MQ=255)
                                                 gTTACAGGGTCACGTTTCCAGTATCGGTCGGGCGATTTATGATCAGAGCGTTGAAAGTGACTCAAGCCt           <  1:1740919/69‑1 (MQ=255)
                                                 gTTACAGGGTCACGTTTCCAGTATCGGTCGGGCGATTTATGACCAGAGCGTTGAAAGTGACTCAAGCCt           <  1:3250075/69‑1 (MQ=255)
                                                 gTTACAGAGTCACGTTTCCAGTATCGGTCGGGCGATTTATGATCAGAGCGTTGAAAGTGACTCAAGCCt           <  1:1456204/69‑1 (MQ=255)
                                                    aCAGGGTCACGTTTCCAGTATCGGTCGGGCGATTTATg                                       <  1:890737/38‑1 (MQ=255)
                                                    aCAGGGTCACGTTTCCAGTATCGGTCGGGCGATTTATg                                       <  1:2944963/38‑1 (MQ=255)
                                                    aCAGGGTCACGTTTCCAGTATCGGTCGGGCGATTTATGATCAGAGCGTTGAAAGTGACTCAAGCCt           >  1:37499/1‑66 (MQ=255)
                                                    aCAGGGTCACGTTTCCAGTATCGGTCGGGCGATTTATGATCAGAGCGTTGAAAGTGACTCAAGCCt           >  1:2567177/1‑66 (MQ=255)
                                                    aCAGGGTCACGTTTCCAGTATCGGTCGGGCGATTTATGATCAGAGCGTTGAAAGTGACTCAAGCCt           >  1:424733/1‑66 (MQ=255)
                                                    aCAGGGTCACGTTTCCAGTATCGGTCGGGCGATTTATGATCAGAGCGTTGAAAGTGACTCAAGCCt           >  1:1631583/1‑66 (MQ=255)
                                                    aCAGGGTCACGTTTCCAGTATCGGTCGGGCGATTTATGATCAGAGCGTTGAAAGTGACTCAAGCCt           >  1:645426/1‑66 (MQ=255)
                                                      aGGGTCACGTGTCCAGTATCGGTCGGGCGATTTATGATCAGAGCGTTGAAAGTGACTCAAGCCTTATTc      >  1:556100/1‑69 (MQ=255)
                                                      aGGGTCACGTGTCCAGTATCGGTCGGGCGATTTATGATCAGAGCGTTGAAAGTGACTCAAGCCTTATTc      >  1:1108772/1‑69 (MQ=255)
                                                      aGGGTCACGTGTCCAGTATCGGTCGGGCGATTTATGATCAGAGCGTTGAAAGTGACTCAAGCCTTATTc      >  1:736836/1‑69 (MQ=255)
                                                      aGGGTCACGTGTCCAGTATCGGTCGGGCGATTTATGATCAGAGCGTTGAAAGTGACTCAAGCCTTATTc      >  1:1124365/1‑69 (MQ=255)
                                                      aGGGTCACGTGTCCAGTATCGGTCGGGCGATTTATGATCAGAGCGTTGAAAGTGACTCAAGCCTTATTc      >  1:2425402/1‑69 (MQ=255)
                                                      aGGGTCACGTGTCCAGTATCGGTCGGGCGATTTATGATCAGAGCGTTGAAAGTGACTCAAGCCTTATTc      >  1:1802387/1‑69 (MQ=255)
                                                      aGGGTCACGTGTCCAGTATCGGTCGGGCGATTTATGATCAGAGCGTTGAAAGTGACTCAAGCCTTATTc      >  1:1760569/1‑69 (MQ=255)
                                                      aGGGTCACGTGTCCAGTATCGGTCGGGCGATTTATGATCAGAGCGTTGAAAGTGACTCAAGCCTTATTc      >  1:274992/1‑69 (MQ=255)
                                                      aGGGTCACGTGTCCAGTATCGGTCGGGCGATTTATGATCAGAGCGTTGAAAGTGACTCAAGCCTTATTc      >  1:291573/1‑69 (MQ=255)
                                                      aGGGTCACGTGTCCAGTATCGGTCGGGCGATTTATGATCAGAGCGTTGAAAGTGACTCAAGCCTTATTc      >  1:3047348/1‑69 (MQ=255)
                                                      aGGGTCACGTGTCCAGTATCGGTCGGGCGATTTATGATCAGAGCGTTGAAAGTGACTCAAGCCTTATTc      >  1:1330887/1‑69 (MQ=255)
                                                      aGGGTCACGTGTCCAGTATCGGTCGGGCGATTTATGATCAGAGCGTTGAAAGTGACTCAAGCCTTATTc      >  1:1852076/1‑69 (MQ=255)
                                                      aGGGTCACGTGTCCAGTATCGGTCGGGCGAATTATGATCAGAGCCTTGAAAGTGACTCAAGCCTTAtt       >  1:1648171/1‑68 (MQ=255)
                                                         gTCACGTTTCCAGTATCGGTCGGGCGATTTATGATCAGAGCg                              <  1:2307285/42‑1 (MQ=255)
                                                         gTCACGTTTCCAGTATCGGTCGGGCGATTTATGATCAGAGCg                              <  1:1665092/42‑1 (MQ=255)
                                                         gTCACGTTTCCAGTATCGGTCGGGCGATTTATGATCAGAGCg                              <  1:2586868/42‑1 (MQ=255)
                                                         gTCACGTTTCCAGTATCGGTCGGGCGATTTATGATCAGAGCg                              <  1:3322741/42‑1 (MQ=255)
                                                          tCACGTTTCCAGTATCGGTCGGGCGATTTATGATCAGAGCGTTGAAAGTGACTCAAGCCt           <  1:1511908/60‑1 (MQ=255)
                                                          tCACGTTTCCAGTATCGGTCGGGCGATTTATGATCAGAGCGTTGAAAGTGACTCAAGCCTTATTCCGGa  >  1:2214320/1‑69 (MQ=255)
                                                          tCACGTTTCCAGTATCGGTCGGGCGATTTATGATCAGAGCGTTGAAAGTGACTCAAGCCTTATTCCGGa  >  1:1860083/1‑69 (MQ=255)
                                                                |                                                              
TCCGCGAAGGTGCACCAGCACAAATTACCCTCTATAGTGATAACAAAACGTTACAGGGTCACGTTTCCAGTATCGGTCGGGCGATTTATGATCAGAGCGTTGAAAGTGACTCAAGCCTTATTCCGGA  >  minE/1049559‑1049685

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