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 2,756,429 T→A 54.3% E130D (GAA→GAT)  rsmB ← 16S rRNA m5C967 methyltransferase, S‑adenosyl‑L‑methionine‑dependent

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,756,4290TA54.3% 29.4 / 146.6 129E130D (GAA→GAT) rsmB16S rRNA m5C967 methyltransferase, S‑adenosyl‑L‑methionine‑dependent
Reads supporting (aligned to +/- strand):  ref base T (35/24);  new base A (17/53);  total (52/77)
Fisher's exact test for biased strand distribution p-value = 6.81e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.58e-01

Only 100 of 135 total aligned reads displayed.

GACGCTTCAGCAACCAGGAAGGATGCAGATAACGTGCATCACTGGCATTAAACTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGTAATACACCGTTTATCAACCCTTTAAGTTGCGGACGCTTAA  >  minE/2756362‑2756493
                                                                   |                                                                
gACGCTTCAGCAACCAGGAAGGATGCAGATAACGTGCATCACTGGCATTAAACTCGGCTAATAACtctt                                                                 <  1:150433/69‑1 (MQ=255)
gACGCTTCAGCAACCAGGAAGGATGCAGATAACGTGCATCACTGGCATTAAACTCGGCTAATAACtctt                                                                 <  1:1485209/69‑1 (MQ=255)
gACGCTTCAGCAACCAGGAAGGATGCAGATAACGTGCATCACTGGCATTAAACTCGGCTAATAACtctt                                                                 <  1:1204165/69‑1 (MQ=255)
gACGCTTCAGCAACCAGGAAGGATGCAGATAACGTGCATCACTGGCATTAAACTCGGCTAATAACtctt                                                                 <  1:2745200/69‑1 (MQ=255)
gACGCTTCAGCAACCAGGAAGGATGCAGATAACGTGCATCACTGGCATTAAACTCGGCTAATAACtctt                                                                 <  1:470851/69‑1 (MQ=255)
gACGCTTCAGCAACCAGGAAGGATGCAGATAACGTGCATCACTGGCATTAAACTCGGCTAATAACtctt                                                                 <  1:1550506/69‑1 (MQ=255)
               aggaaggaTGCAGATAACGTGCATCACTGGCATTAAACTCGGCTAATAACTCTTCTTGCTGACGCTGGa                                                  <  1:3235087/69‑1 (MQ=255)
               aggaaggaTGCAGATAACGTGCATCACTGGCATTAAACTCGGCTAATAACTCTTCTTGCTGACGCTGGa                                                  <  1:3164680/69‑1 (MQ=255)
                   aggaTGCAGATAACGTGCATCACTGGCATTAAACTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTg                                              >  1:1009924/1‑69 (MQ=255)
                   aggaTGCAGATAACGTGCATCACTGGCATTAAACTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTg                                              >  1:2346168/1‑69 (MQ=255)
                   aggaTGCAGATAACGTGCATCACTGGCATTAAACTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTg                                              >  1:84254/1‑69 (MQ=255)
                   aggaTGCAGATAACGTGCATCACTGGCATTAAACTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTg                                              >  1:1143089/1‑69 (MQ=255)
                   aggaTGCAGATAACGTGCATCACTGGCATTAAACTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTg                                              >  1:275442/1‑69 (MQ=255)
                   aggaTGCAGATAACGTGCATCACTGGCATTAAACTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTg                                              >  1:3266784/1‑69 (MQ=255)
                        gCAGATAACGTGCATCACTGGCATTAAACTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGTa                                         <  1:534359/69‑1 (MQ=255)
                        gCAGATAACGTGCATCACTGGCATTAAACTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGTa                                         <  1:1433205/69‑1 (MQ=255)
                        gCAGATAACGTGCATCACTGGCATTAAACTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGTa                                         <  1:1831173/69‑1 (MQ=255)
                        gCAGATAACGTGCATCACTGGCATTAAACTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGTa                                         <  1:1919500/69‑1 (MQ=255)
                        gCAGATAACGTGCATCACTGGCATTAAACTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGTa                                         <  1:2132172/69‑1 (MQ=255)
                         cAGATAACGTGCATCACTGGCATTAAACTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGTaa                                        >  1:2244445/1‑69 (MQ=255)
                         cAGATAACGTGCATCACTGGCATTAAACTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGTaa                                        >  1:3347733/1‑69 (MQ=255)
                            aTAACGTGCATCACTGGCATTAAACTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGTAATac                                     <  1:224446/69‑1 (MQ=255)
                             tAACGTGCATCACTGGCATTAAACTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGTAATaca                                    >  1:384313/1‑69 (MQ=255)
                             tAACGTGCATCACTGGCATTAAACTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGTAATaca                                    <  1:3132318/69‑1 (MQ=255)
                             tAACGTGCATCACTGGCATTAAACTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGTAATaca                                    <  1:13194/69‑1 (MQ=255)
                             tAACGTGCATCACTGGCATTAAACTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGTAATaca                                    >  1:725185/1‑69 (MQ=255)
                                 gTGCATCACTGGCATTAAACTCGGCTAATAACTCATCTTGCTGACGCTGTAAc                                                <  1:1010585/53‑1 (MQ=39)
                                 gTGCATCACTGGCATTAAACTCGGCTAATAACTCATCTTGCTGACGCTGGAAc                                                <  1:964733/53‑1 (MQ=255)
                                 gTGCATCACTGGCATTAAACTCGGCTAATAACTCATCTTGCTGACGCTGGAAc                                                <  1:2322106/53‑1 (MQ=255)
                                 gTGCATCACTGGCATTAAACTCGGCTAATAACTCATCTTGCTGACGCTGGAAc                                                <  1:900866/53‑1 (MQ=255)
                                 gTGCATCACTGGCATTAAACTCGGCTAATAACTCATCTTGCTGACGCTGGAAc                                                <  1:2414073/53‑1 (MQ=255)
                                 gTGCATCACTGGCATTAAACTCGGCTAATAACTCATCTTGCTGACGCTGGAAc                                                <  1:2491780/53‑1 (MQ=255)
                                 gTGCATCACTGGCATTAAACTCGGCTAATAACTCATCTTGCTGACGCTGGAAc                                                <  1:821098/53‑1 (MQ=255)
                                 gTGCATCACTGGCATTAAACTCGGCTAATAACTCATCTTGCTGACGCTGGAAc                                                <  1:258940/53‑1 (MQ=255)
                                 gTGCATCACTGGCATTAAACTCGGCTAATAACTCATCTTGCTGACGCTGGAAc                                                <  1:2722555/53‑1 (MQ=255)
                                 gTGCATCACTGGCATTAAACTCGGCTAATAACTCATCTTGCTGACGCTGGAAc                                                <  1:7678/53‑1 (MQ=255)
                                 gTGCATCACTGGCATTAAACTCGGCTAATAACTCATCTTGCTGACGCTGGAAc                                                <  1:2874034/53‑1 (MQ=255)
                                 gTGCATCACTGGCATTAAACTCGGCTAATAACTCATCTTGCTGACGCTGGAAc                                                <  1:1193741/53‑1 (MQ=255)
                                 gTGCATCACTGGCATTAAACTCGGCTAATAACTCATCTTGCTGACGCTGGAAc                                                <  1:1725943/53‑1 (MQ=255)
                                 gTGCATCACTGGCATTAAACTCGGCTAATAACTCATCTTGCTGACGCTGGAAc                                                <  1:1552526/53‑1 (MQ=255)
                                 gTGCATCACTGGCATTAAACTCGGCTAATAACTCATCTTGCTGACGCTGGAAc                                                <  1:1348603/53‑1 (MQ=255)
                                 gTGCATCACTGGCATTAAACTCGGCTAATAACTCATCTTGCTGACGCTGGAAc                                                <  1:1360341/53‑1 (MQ=255)
                                 gTGCATCACTGGCATTAAACTCGGCTAATAACTCATCTTGCTGACGCTGGAAc                                                <  1:1905940/53‑1 (MQ=255)
                                 gTGCATCACCGGCATTAAACTCGGCTAATAACTCATCTTGCTGACGCTGGAAc                                                <  1:1359353/53‑1 (MQ=255)
                                        aCTGGCATTAAACTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGTAATACACGGTTTATc                           >  1:1387994/1‑67 (MQ=255)
                                        aCTGGCATTAAACTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGTAATACACCGTTTATc                           >  1:3266021/1‑67 (MQ=255)
                                        aCTGGCATTAAACTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGTAATACACCGTTTATCaa                         >  1:962769/1‑69 (MQ=255)
                                        aCTGGCATTAAACTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGTAATACACCGTTTATCaa                         >  1:1268645/1‑69 (MQ=255)
                                        aCTGGCATTAAACTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGTAATACACCGTTTATCaa                         >  1:2660656/1‑69 (MQ=255)
                                        aCTGGCATTAAACTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGTAATACACCGTTTATCa                          >  1:3291579/1‑68 (MQ=255)
                                        aCTGGCATTAAACTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGTAATACACCGTATATc                           >  1:3317353/1‑67 (MQ=255)
                                              aTTAAACTCGGCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGTTAATCAAtccct                    <  1:202323/68‑3 (MQ=255)
                                              aTTAAACTCGGCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGTTAATCAAtccct                    <  1:3213334/68‑3 (MQ=255)
                                              aTTAAACTCGGCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGTTAATCAAtccct                    <  1:1294275/68‑3 (MQ=255)
                                              aTTAAACTCGGCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGTTAATCAAtccct                    <  1:2122120/68‑3 (MQ=255)
                                              aTTAAACTCGGCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGTTAATCAAtccct                    <  1:3146924/68‑3 (MQ=255)
                                                 aaaCTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGt                                          <  1:2192675/43‑1 (MQ=255)
                                                 aaaCTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGt                                          <  1:3111019/43‑1 (MQ=255)
                                                 aaaCTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGt                                          <  1:3032041/43‑1 (MQ=255)
                                                 aaaCTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGt                                          <  1:2946089/43‑1 (MQ=255)
                                                 aaaCTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGt                                          <  1:2472530/43‑1 (MQ=255)
                                                 aaaCTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGt                                          <  1:2788511/43‑1 (MQ=255)
                                                 aaaCTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGt                                          <  1:2593002/43‑1 (MQ=255)
                                                 aaaCTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGt                                          <  1:277698/43‑1 (MQ=255)
                                                 aaaCTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGTAATACAcc                                  >  1:3008934/1‑51 (MQ=255)
                                                 aaaCTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGTAATACACCGTTTATCAACCCTTTAAg                >  1:2900158/1‑69 (MQ=255)
                                                 aaaCTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGTAATACACCGTTTATCAACCCTTTAAg                >  1:2011646/1‑69 (MQ=255)
                                                 aaaCTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGTAATACACCGTTTATCAACCCTTTAAg                >  1:1771175/1‑69 (MQ=255)
                                                  aaCTCGGCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGtt                               <  1:2353797/53‑1 (MQ=255)
                                                  aaCTCGGCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGtt                               <  1:2423162/53‑1 (MQ=255)
                                                  aaCTCGGCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGtt                               <  1:341348/53‑1 (MQ=255)
                                                  aaCTCGGCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGtt                               <  1:25012/53‑1 (MQ=255)
                                                  aaCTCGGCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGtt                               <  1:604930/53‑1 (MQ=255)
                                                  aaCTCGGCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGtt                               <  1:782035/53‑1 (MQ=255)
                                                  aaCTCGGCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGtt                               <  1:1516756/53‑1 (MQ=255)
                                                  aaCTCGGCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGtt                               <  1:2744062/53‑1 (MQ=255)
                                                  aaCTCGGCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGtt                               <  1:1183459/53‑1 (MQ=255)
                                                  aaCTCGGCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGtt                               <  1:1108486/53‑1 (MQ=255)
                                                  aaCTCGGCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGtt                               <  1:90363/53‑1 (MQ=255)
                                                       ggCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGTTAATCa                          >  1:2175184/1‑53 (MQ=255)
                                                       ggCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGTTAATCa                          >  1:1133030/1‑53 (MQ=255)
                                                       ggCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGTTAATCa                          >  1:862744/1‑53 (MQ=255)
                                                       ggCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGTTAATCa                          >  1:90237/1‑53 (MQ=255)
                                                       ggCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGTTAATCa                          >  1:2216327/1‑53 (MQ=255)
                                                       ggCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGTTAATCa                          >  1:596296/1‑53 (MQ=255)
                                                       ggCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGTTAATCa                          >  1:2936825/1‑53 (MQ=255)
                                                       ggCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGTTAATCa                          >  1:500621/1‑53 (MQ=255)
                                                       ggCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGTTAATCa                          >  1:2513501/1‑53 (MQ=255)
                                                       ggCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGTTAATCa                          >  1:1887824/1‑53 (MQ=255)
                                                       ggCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGTTAATCa                          >  1:3261252/1‑53 (MQ=255)
                                                       ggCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGTTAATCa                          >  1:1588931/1‑53 (MQ=255)
                                                       ggCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGTTAATCa                          >  1:3116577/1‑53 (MQ=255)
                                                       ggCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGTTAATCa                          >  1:2811800/1‑53 (MQ=255)
                                                        gCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGt                                          <  1:3018353/36‑1 (MQ=255)
                                                               aCTCTTCTTGCTGACGCTGGAACTGGCGTAATACACCGTTTATCAACCCTTTAAGTTGCGGACGCTTaa  >  1:593708/1‑69 (MQ=255)
                                                               aCTCTTCTTGCTGACGCTGGAACTGGCGTAATACACCGTTTATCAACCCTTTAAGTTGCGGACGCTTaa  >  1:2109202/1‑69 (MQ=255)
                                                               aCTCTTCTTGCTGACGCTGGAACTGGCGTAATACACCGTTTATCAACCCTTTAAGTTGCGGACGCTTaa  >  1:3057908/1‑69 (MQ=255)
                                                               aCTCTTCTTGCTGACGCTGGAACTGGCGTAATACACCGTTTATCAACCCTTTAAGTTGCGGACGCTTaa  >  1:3054266/1‑69 (MQ=255)
                                                               aCTCTTCTTGCTGACGCTGGAACTGGCGTAATACACCGTTTATCAACCCTTTAAGTTGCGGACGCTTaa  >  1:1699742/1‑69 (MQ=255)
                                                               aCTCTTCTTGCTGACGCTGGAACTGGCGTAATACACCGTTTATCAACCCTTTAAGTTGCGGACGCTTaa  >  1:1037296/1‑69 (MQ=255)
                                                                   |                                                                
GACGCTTCAGCAACCAGGAAGGATGCAGATAACGTGCATCACTGGCATTAAACTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGTAATACACCGTTTATCAACCCTTTAAGTTGCGGACGCTTAA  >  minE/2756362‑2756493

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