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 2,756,450 G→A 48.1% R123R (CGC→CGT)  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
*minE2,756,4500GA48.1% 8.7 / 92.1 106R123R (CGC→CGT) rsmB16S rRNA m5C967 methyltransferase, S‑adenosyl‑L‑methionine‑dependent
Reads supporting (aligned to +/- strand):  ref base G (27/28);  new base A (17/34);  total (44/62)
Fisher's exact test for biased strand distribution p-value = 1.17e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 106 total aligned reads displayed.

TGCAGATAACGTGCATCACTGGCATTAAACTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGTAATACACCGTTTATCAACCCTTTAAGTTGCGGACGCTTAATTGCGATAGCGCC  >  minE/2756385‑2756506
                                                                 |                                                        
tGCAGATAACGTGCATCACTGGCATTAAACTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGt                                                       >  1:2698700/1‑69 (MQ=255)
 gCAGATAACGTGCATCACTGGCATTAAACTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGTa                                                      <  1:1433205/69‑1 (MQ=255)
 gCAGATAACGTGCATCACTGGCATTAAACTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGTa                                                      <  1:534359/69‑1 (MQ=255)
 gCAGATAACGTGCATCACTGGCATTAAACTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGTa                                                      <  1:1831173/69‑1 (MQ=255)
 gCAGATAACGTGCATCACTGGCATTAAACTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGTa                                                      <  1:2132172/69‑1 (MQ=255)
 gCAGATAACGTGCATCACTGGCATTAAACTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGTa                                                      <  1:1919500/69‑1 (MQ=255)
  cAGATAACGTGCATCACTGGCATTAAACTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGTaa                                                     >  1:3347733/1‑69 (MQ=255)
  cAGATAACGTGCATCACTGGCATTAAACTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGTaa                                                     >  1:2244445/1‑69 (MQ=255)
     aTAACGTGCATCACTGGCATTAAACTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGTAATac                                                  <  1:224446/69‑1 (MQ=255)
      tAACGTGCATCACTGGCATTAAACTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGTAATaca                                                 >  1:725185/1‑69 (MQ=255)
      tAACGTGCATCACTGGCATTAAACTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGTAATaca                                                 >  1:384313/1‑69 (MQ=255)
      tAACGTGCATCACTGGCATTAAACTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGTAATaca                                                 <  1:13194/69‑1 (MQ=255)
            gCATCACTGGCATTAAACTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGTa                                                      <  1:149287/58‑1 (MQ=255)
                 aCTGGCATTAAACTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGTAATACACGGTTTATc                                        >  1:1387994/1‑67 (MQ=255)
                 aCTGGCATTAAACTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGTAATACACCGTTTATc                                        >  1:3266021/1‑67 (MQ=255)
                 aCTGGCATTAAACTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGTAATACACCGTTTATCaa                                      >  1:962769/1‑69 (MQ=255)
                 aCTGGCATTAAACTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGTAATACACCGTTTATCaa                                      >  1:2660656/1‑69 (MQ=255)
                 aCTGGCATTAAACTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGTAATACACCGTTTATCaa                                      >  1:1268645/1‑69 (MQ=255)
                 aCTGGCATTAAACTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGTAATACACCGTTTATCa                                       >  1:3291579/1‑68 (MQ=255)
                 aCTGGCATTAAACTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGTAATACACCGTATATc                                        >  1:3317353/1‑67 (MQ=255)
                       aTTAAACTCGGCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGTTAATCAAtccct                                 <  1:3213334/68‑3 (MQ=255)
                       aTTAAACTCGGCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGTTAATCAAtccct                                 <  1:1294275/68‑3 (MQ=255)
                       aTTAAACTCGGCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGTTAATCAAtccct                                 <  1:867393/68‑3 (MQ=255)
                       aTTAAACTCGGCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGTTAATCAAtccct                                 <  1:2122120/68‑3 (MQ=255)
                       aTTAAACTCGGCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGTTAATCAAtccct                                 <  1:202323/68‑3 (MQ=255)
                       aTTAAACTCGGCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGTTAATCAAtccct                                 <  1:3146924/68‑3 (MQ=255)
                          aaaCTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGt                                                       <  1:2472530/43‑1 (MQ=255)
                          aaaCTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGt                                                       <  1:122383/43‑1 (MQ=255)
                          aaaCTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGt                                                       <  1:277698/43‑1 (MQ=255)
                          aaaCTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGt                                                       <  1:2192675/43‑1 (MQ=255)
                          aaaCTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGt                                                       <  1:2788511/43‑1 (MQ=255)
                          aaaCTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGt                                                       <  1:2946089/43‑1 (MQ=255)
                          aaaCTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGt                                                       <  1:3111019/43‑1 (MQ=255)
                          aaaCTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGt                                                       <  1:3032041/43‑1 (MQ=255)
                          aaaCTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGTAATACAcc                                               >  1:3008934/1‑51 (MQ=255)
                          aaaCTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGTAATACACCGTTTATCAACCCTTTAAg                             >  1:2900158/1‑69 (MQ=255)
                          aaaCTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGTAATACACCGTTTATCAACCCTTTAAg                             >  1:2011646/1‑69 (MQ=255)
                          aaaCTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGTAATACACCGTTTATCAACCCTTTAAg                             >  1:394218/1‑69 (MQ=255)
                          aaaCTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGTAATACACCGTTTATCAACCCTTTAAg                             >  1:3272867/1‑69 (MQ=255)
                          aaaCTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGTAATACACCGTTTATCAACCCTTTAAg                             >  1:1771175/1‑69 (MQ=255)
                           aaCTCGGCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGtt                                            <  1:2744062/53‑1 (MQ=255)
                           aaCTCGGCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGtt                                            <  1:2961392/53‑1 (MQ=255)
                           aaCTCGGCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGtt                                            <  1:2571836/53‑1 (MQ=255)
                           aaCTCGGCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGtt                                            <  1:25012/53‑1 (MQ=255)
                           aaCTCGGCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGtt                                            <  1:604930/53‑1 (MQ=255)
                           aaCTCGGCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGtt                                            <  1:564799/53‑1 (MQ=255)
                           aaCTCGGCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGtt                                            <  1:2353797/53‑1 (MQ=255)
                           aaCTCGGCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGtt                                            <  1:341348/53‑1 (MQ=255)
                           aaCTCGGCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGtt                                            <  1:1159358/53‑1 (MQ=255)
                           aaCTCGGCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGtt                                            <  1:90363/53‑1 (MQ=255)
                           aaCTCGGCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGtt                                            <  1:1183459/53‑1 (MQ=255)
                           aaCTCGGCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGtt                                            <  1:1820042/53‑1 (MQ=255)
                           aaCTCGGCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGtt                                            <  1:2080082/53‑1 (MQ=255)
                           aaCTCGGCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGtt                                            <  1:782035/53‑1 (MQ=255)
                           aaCTCGGCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGtt                                            <  1:1108486/53‑1 (MQ=255)
                           aaCTCGGCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGtt                                            <  1:3243064/53‑1 (MQ=255)
                           aaCTCGGCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGtt                                            <  1:2217038/53‑1 (MQ=255)
                           aaCTCGGCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGtt                                            <  1:724823/53‑1 (MQ=255)
                           aaCTCGGCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGtt                                            <  1:2423162/53‑1 (MQ=255)
                                ggCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGTTAATCa                                       >  1:3261252/1‑53 (MQ=255)
                                ggCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGTTAATCa                                       >  1:3116577/1‑53 (MQ=255)
                                ggCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGTTAATCa                                       >  1:1133030/1‑53 (MQ=255)
                                ggCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGTTAATCa                                       >  1:500621/1‑53 (MQ=255)
                                ggCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGTTAATCa                                       >  1:2513501/1‑53 (MQ=255)
                                ggCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGTTAATCa                                       >  1:2936825/1‑53 (MQ=255)
                                ggCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGTTAATCa                                       >  1:2811800/1‑53 (MQ=255)
                                ggCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGTTAATCa                                       >  1:596296/1‑53 (MQ=255)
                                ggCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGTTAATCa                                       >  1:2284221/1‑53 (MQ=255)
                                ggCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGTTAATCa                                       >  1:2216327/1‑53 (MQ=255)
                                ggCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGTTAATCa                                       >  1:2175184/1‑53 (MQ=255)
                                ggCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGTTAATCa                                       >  1:1332157/1‑53 (MQ=255)
                                ggCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGTTAATCa                                       >  1:862744/1‑53 (MQ=255)
                                ggCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGTTAATCa                                       >  1:1887824/1‑53 (MQ=255)
                                ggCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGTTAATCa                                       >  1:90237/1‑53 (MQ=255)
                                ggCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGTTAATCa                                       >  1:919592/1‑53 (MQ=255)
                                ggCTAATAACTCATCTTGCTGACGCTGGAACTGACGTAATACACCGTTAATCa                                       >  1:1588931/1‑53 (MQ=255)
                                 gCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGt                                                       <  1:3018353/36‑1 (MQ=255)
                                        aCTCTTCTTGCTGACGCTGGAACTGGCGTAATACACCGTTTATCAACCCTTTAAGTTGCGGAc                     >  1:1684916/1‑63 (MQ=255)
                                        aCTCTTCTTGCTGACGCTGGAACTGGCGTAATACACCGTTTATCAACCCTTTAAGTTGCGGACGCTTaa               >  1:593708/1‑69 (MQ=255)
                                        aCTCTTCTTGCTGACGCTGGAACTGGCGTAATACACCGTTTATCAACCCTTTAAGTTGCGGACGCTTaa               >  1:1037296/1‑69 (MQ=255)
                                        aCTCTTCTTGCTGACGCTGGAACTGGCGTAATACACCGTTTATCAACCCTTTAAGTTGCGGACGCTTaa               >  1:3157356/1‑69 (MQ=255)
                                        aCTCTTCTTGCTGACGCTGGAACTGGCGTAATACACCGTTTATCAACCCTTTAAGTTGCGGACGCTTaa               >  1:3057908/1‑69 (MQ=255)
                                        aCTCTTCTTGCTGACGCTGGAACTGGCGTAATACACCGTTTATCAACCCTTTAAGTTGCGGACGCTTaa               >  1:3054266/1‑69 (MQ=255)
                                        aCTCTTCTTGCTGACGCTGGAACTGGCGTAATACACCGTTTATCAACCCTTTAAGTTGCGGACGCTTaa               >  1:1699742/1‑69 (MQ=255)
                                        aCTCTTCTTGCTGACGCTGGAACTGGCGTAATACACCGTTTATCAACCCTTTAAGTTGCGGACGCTTaa               >  1:2109202/1‑69 (MQ=255)
                                        aCTCATCTTGCTGACGCTGGAACTGACGTAATACACCGTTAATCAAtccct                                 <  1:1363903/51‑3 (MQ=255)
                                              cttGCTGACGCTGGAACTGGCGTAATACACCGTTTATCAACCCTTTAAGTTGCGGACGCTTAATTGc           <  1:476676/67‑1 (MQ=255)
                                              cttGCTGACGCTGGAACTGGCGTAATACACCGTTTATCAACCCTTTAAGTTGCGGACGCTTAATTGc           <  1:1023512/67‑1 (MQ=255)
                                              cttGCTGACGCTGGAACTGGCGTAATACACCGTTTATCAACCCTTTAAGTTGCGGACGCTTAATTGc           <  1:2492605/67‑1 (MQ=255)
                                              cttGCTGACGCTGGAACTGGCGTAATACACCGTTTATCAACCCTTTAAGTTGCGGACGCTTAATTGc           <  1:227503/67‑1 (MQ=255)
                                                    gACGCTGGAACTGACGTAATACACCGTTAATCAATCCCTTAAGTTGCGGGCGCTTAAt              <  1:1198911/58‑1 (MQ=255)
                                                    gACGCTGGAACTGACGTAATACACCGTTAATCAATCCCTTAAGTTGCGGGCGCTTAAt              <  1:1655114/58‑1 (MQ=255)
                                                    gACGCTGGAACTGACGTAATACACCGTTAATCAATCCCTTAAGTTGCGGGCGCTTAAt              <  1:1676372/58‑1 (MQ=255)
                                                    gACGCTGGAACTGACGTAATACACCGTTAATCAATCCCTTAAGTTGCGGGCGCTTAAt              <  1:1429955/58‑1 (MQ=255)
                                                    gACGCTGGAACTGACGTAATACACCGTTAATCAATCCCTTAAGTTGCGGGCGCTTAAt              <  1:2209479/58‑1 (MQ=255)
                                                    gACGCTGGAACTGACGTAATACACCGTTAATCAATCCCTTAAGTTGCGGGCGCTTAAt              <  1:606395/58‑1 (MQ=255)
                                                       gCTGGAACTGGCGTAATACACCGTTTATCAACCCTTTAAGTTGCGGACGCTTAATTGCTATAGCGcc  <  1:3401015/67‑1 (MQ=255)
                                                       gCTGGAACTGGCGTAATACACCGTTTATCAACCCTTTAAGTTGCGGACGCTTAATTGCGATAGCGcc  <  1:808027/67‑1 (MQ=255)
                                                       gCTGGAACTGGCGTAATACACCGTTTATCAACCCTTTAAGTTGCGGACGCTTAATTGCGATAGCGcc  <  1:317264/67‑1 (MQ=255)
                                                       gCTGGAACTGGCGTAATACACCGTTTATCAACCCTTTAAGTTGCGGACGCTTAATTGCGATAGCGcc  <  1:1609955/67‑1 (MQ=255)
                                                                 |                                                        
TGCAGATAACGTGCATCACTGGCATTAAACTCGGCTAATAACTCTTCTTGCTGACGCTGGAACTGGCGTAATACACCGTTTATCAACCCTTTAAGTTGCGGACGCTTAATTGCGATAGCGCC  >  minE/2756385‑2756506

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