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 2,002,578 C→T 24.2% V49V (GTG→GTA)  hybG ← hydrogenase 2 accessory protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,002,5780CT24.2% 105.6 / 26.0 82V49V (GTG→GTA) hybGhydrogenase 2 accessory protein
Reads supporting (aligned to +/- strand):  ref base C (44/18);  new base T (9/11);  total (53/29)
Fisher's exact test for biased strand distribution p-value = 5.79e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.95e-01

GCGTCTAATGTGGCTTTGGCTTCATCTTCGTCGATGATGCTCATGGCAAATCCGACGTGTACCAGCACCCACTGGCCCAGTAGATCGGCAGGGTTACCTTCACAAATCAGGGCGATATTCACATCGCGCTTGAT  >  minE/2002513‑2002646
                                                                 |                                                                    
gCGTCTAATGTGGCTTTGGCTTCATCTTCGTCGATGATGCTCATGGCAAATCCGACGTGTACCAGCAcc                                                                   >  1:1868867/1‑69 (MQ=255)
gCGTCTAATGTGGCTTTGGCTTCATCTTCGTCGATGATGCTCATGGCAAATCCGACGTGTACCAGCAcc                                                                   <  1:2338961/69‑1 (MQ=255)
gCGTCTAATGTGGCTTTGGCTTCATCTTCGTCGATGATGCTCATGGCAAATCCGACGTGTACCAGCAcc                                                                   <  1:2318728/69‑1 (MQ=255)
gCGTCTAATGTGGCTTTGGCTTCATCTTCGTCGATGATGCTCATGGCAAATCCGACGTGTACCAGCAcc                                                                   <  1:1329656/69‑1 (MQ=255)
gCGTCTAATGTGGCTTTGGCTTCATCTTCGTCGATGATGCTCATGGCAAATCCGACGTGTACCAGCAcc                                                                   >  1:3083184/1‑69 (MQ=255)
gCGTCTAATGTGGCTTTGGCTTCATCTTCGTCGATGATGCTCATGGCAAATCCGACGTGTACCAGCAcc                                                                   <  1:2284250/69‑1 (MQ=255)
gCGTCTAATGTGGCTTTGGCTTCATCTTCGTCGATGATGCTCATGGCAAATCCGACGTGTACCAGCAcc                                                                   <  1:980342/69‑1 (MQ=255)
 cGTCTAATGTGGCTTTGGCTTCATCTTCGTCGATGATGCTCATGGCAAATCCGACGTGTACCAGCAccc                                                                  >  1:2230974/1‑69 (MQ=255)
 cGTCTAATGTGGCTTTGGCTTCATCTTCGTCGATGATGCTCATGGCAAATCCGACGTGTACCAGCAccc                                                                  >  1:648577/1‑69 (MQ=255)
     tAATGTGGCTTTGGCTTCATCTTCGTCGATGATGCTCATGGCAAATCCGACGTGTACCAGCACCCACt                                                               >  1:1692064/1‑68 (MQ=255)
     tAATGTGGCTTTGGCTTCATCTTCGTCGATGATGCTCATGGCAAATCCGACGTGTACCAGCACCCACTg                                                              >  1:2337516/1‑69 (MQ=255)
     tAATGTGGCTTTGGCTTCATCTTCGTCGATGATGCTCATGGCAAATCCGACGTGTACCAGCACCCACTg                                                              >  1:3253688/1‑69 (MQ=255)
     tAATGTGGCTTTGGCTTCATCTTCGTCGATGATGCTCATGGCAAATCCGACGTGTACCAGCACCCACTg                                                              >  1:3266060/1‑69 (MQ=255)
     tAATGTGGCTTTGGCTTCATCTTCGTCGATGATGCTCATGGCAAATCCGACGTGTACCAGCACCCACTg                                                              >  1:3274768/1‑69 (MQ=255)
     tAATGTGGCTTTGGCTTCATCTTCGTCGATGATGCTCATGGCAAATCCGACGTGTACCAGCACCCACTg                                                              >  1:2338806/1‑69 (MQ=255)
     tAATGTGGCTTTGGCTTCATCTTCGTCGATGATGCTCATGGCAAATCCGACGTGTACCAGCACCCACTg                                                              >  1:2564716/1‑69 (MQ=255)
     tAATGTGGCTTTGGCTTCATCTTCGTCGATGATGCTCATGGCAAATCCGACGTGTACCAGCACCCACTg                                                              >  1:2837271/1‑69 (MQ=255)
     tAATGTGGCTTTGGCTTCATCTTCGTCGATGATGCTCATGGCAAATCCGACGTGTACCAGCACCCACTg                                                              >  1:830087/1‑69 (MQ=255)
     tAATGTGGCTTTGGCTTCATCTTCGTCGATGATGCTCATGGCAAATCCGACGTGTACCAGCACCCACTg                                                              >  1:666968/1‑69 (MQ=255)
     tAATGTGGCTTTGGCTTCATCTTCGTCGATGATGCTCATGGCAAATCCGACGTGTACCAGCACCCACTg                                                              >  1:1423202/1‑69 (MQ=255)
     tAATGTGGCTTTGGCTTCATCTTCGTCGATGATGCTCATGGCAAATCCGACGTGTACCAGCACCCACTg                                                              >  1:80651/1‑69 (MQ=255)
     tAATGTGGCTTTGGCTTCATCTTCGTCGATGATGCTCATGGCAAATCCGACGTGTACCAGCACCCACTg                                                              >  1:1549436/1‑69 (MQ=255)
     tAATGTGGCTTTGGCTTCATCTTCGTCGATGATGCTCATGGCAAATCCGACGTGTACCAGCACCCACTg                                                              >  1:462654/1‑69 (MQ=255)
          tggctttggcttCATCTTCGTCGATGATGCTCGTGGCAAATCCGACGTGTACCAGCACCCACTGGccc                                                          >  1:2922619/1‑68 (MQ=255)
          tggctttggcttCATCTTCGTCGATGATGCTCATGGCAAATCCGACGTGTACCAGCACCCACTGGccc                                                          >  1:166315/1‑68 (MQ=255)
          tggctttggcttCATCTTCGTCGATGATGCTCATGGCAAATCCGACGTGTACCAGCACCCACTGGccc                                                          >  1:714501/1‑68 (MQ=255)
          tggctttggcttCATCTTCGTCGATGATGCTCATGGCAAATCCGACGTGTACCAGCACCCACTGGccc                                                          >  1:124352/1‑68 (MQ=255)
          tggctttggcttCATCTTCGTCGATGATGCTCATGGCAAATCCGACGTGTACCAGCACCCACTGGccc                                                          >  1:95305/1‑68 (MQ=255)
          tggctttggcttCATCTTCGTCGATGATGCTCATGGCAAATCCGACGTGTACCAGCACCCACTGGccc                                                          >  1:3308715/1‑68 (MQ=255)
          tggctttggcttCATCTTCGTCGATGATGCTCATGGCAAATCCGACGTGTACCAGCACCCACTGGccc                                                          >  1:1787740/1‑68 (MQ=255)
              tttggcttCGTCTTCATCGATAATGCTCATGGCAAATCCGACGTGTACCAGTACCCACTGGCCcagcag                                                     <  1:218259/69‑1 (MQ=255)
              tttggcttCGTCTTCATCGATAATGCTCATGGCAAATCCGACGTGTACCAGTACCCACTGGCCcagcag                                                     <  1:2852910/69‑1 (MQ=255)
              tttggcttCGTCTTCATCGATAATGCTCATGGCAAATCCGACGTGTACCAGTACCCACTGGCCcagcag                                                     <  1:2908981/69‑1 (MQ=255)
              tttggcttCGTCTTCATCGATAATGCTCATGGCAAATCCGACGTGTACCAGTACCCACTGGCCcagcag                                                     <  1:2301115/69‑1 (MQ=255)
              tttggcttCGTCTTCATCGATAATGCTCATGGCAAATCCGACGTGTACCAGTACCCACTGGCCcagcag                                                     <  1:3017610/69‑1 (MQ=255)
              tttggcttCGTCTTCATCGATAATGCTCATGGCAAATCCGACGTGTACCAGTACCCACTGGCCcagcag                                                     <  1:693106/69‑1 (MQ=255)
              tttggcttCGTCTTCATCGATAATGCTCATGGCAAATCCGACGTGTACCAGTACCCACTGGCCcagcag                                                     <  1:1663803/69‑1 (MQ=255)
               ttggcttCGTCTTCATCGATAATGCTCATGGCAAATCCGACGTGTACCAGTACCCACTGGCCcagcag                                                     <  1:1855410/68‑1 (MQ=255)
               ttggcttCGTCTTCATCGATAATGCTCATGGCAAATCCGACGTGTACCAGTACCCACTGGCCcagcag                                                     <  1:3145728/68‑1 (MQ=255)
               ttggcttCGTCTTCATCGATAATGCTCATGGCAAATCCGACGTGTACCAGTACCCACTGGCCcagcag                                                     <  1:717200/68‑1 (MQ=255)
               ttggcttCATCTTCGTCGATGATGCTCATGGCAAATCCGACGTGTACCAGCACCCACTGGccc                                                          >  1:3206768/1‑63 (MQ=255)
               ttggcttCATCTTCGTCGATGATGCTCATGGCAAATCCGACGTGTACCAGCACCCACTGGccc                                                          >  1:613511/1‑63 (MQ=255)
               ttggcttCATCTTCGTCGATGATGCTCATGGCAAATCCGACGTGTACCAGCACCCACTGGccc                                                          >  1:1408852/1‑63 (MQ=255)
               ttggcttCATCTTCGTCGATGATGCTCATGGCAAATCCGACGTGTACCAGCACCCACTGGccc                                                          >  1:1330846/1‑63 (MQ=255)
                tggcttCGTCTTCATCGATAATGCTCATGGCAAATCCGACGTGTACCAGTACCCACTGGCCcagcag                                                     <  1:3230100/67‑1 (MQ=255)
                 ggcttCGTCTTCATCGATAATGCTCATGGCAAATCCGACGTGTACCAGTACCCACTGGCCCAGCAGAtg                                                  >  1:929938/1‑68 (MQ=255)
                 ggcttCGTCTTCATCGATAATGCTCATGGCAAATCCGACGTGTACCAGTACCCACTGGCCCAGCAGATc                                                  >  1:1010172/1‑69 (MQ=255)
                 ggcttCGTCTTCATCGATAATGCTCATGGCAAATCCGACGTGTACCAGTACCCACTGGCCCAGCAGATc                                                  >  1:3316086/1‑69 (MQ=255)
                 ggcttCGTCTTCATCGATAATGCTCATGGCAAATCCGACGTGTACCAGTACCCACTGGCCCAGCAGATc                                                  >  1:3321076/1‑69 (MQ=255)
                 ggcttCGTCTTCATCGATAATGCTCATGGCAAATCCGACGTGTACCAGTACCCACTGGCCCAGCAGATc                                                  >  1:994772/1‑69 (MQ=255)
                 ggcttCGTCTTCATCGATAATGCTCATGGCAAATCCGACGTGTACCAGTACCCACTGGCCCAGCAGATc                                                  >  1:2458368/1‑69 (MQ=255)
                 ggcttCGTCTTCATCGATAATGCTCATGGCAAATCCGACGTGTACCAGTACCCACTGGCCCAGCAGATc                                                  >  1:2999074/1‑69 (MQ=255)
                 ggcttCGTCTTCATCGATAATGCTCATGGCAAATCCGACGTGTACCAGTACCCACTGGCCCAGCAGATc                                                  >  1:1816961/1‑69 (MQ=255)
                 ggcttCGTCTTCATCGATAATGCTCATGGCAAATCAGACGTGTACCAGTACCCACTGGCCCAGCAGATc                                                  >  1:68171/1‑69 (MQ=255)
                    ttCATCTTCGTCGATGATGCTCATGGCAAATCCGACGTGTACCAGCACCCACTGGCCCAGTAg                                                     >  1:2731376/1‑63 (MQ=255)
                    ttCATCTTCGTCGATGATGCTCATGGCAAATCCGACGTGTACCAGCACCCACTGGCCCAGTAg                                                     <  1:1408976/63‑1 (MQ=255)
                    ttCATCTTCGTCGATGATGCTCATGGCAAATCCGACGTGTACCAGCACCCACTGGCCCAGTAg                                                     >  1:2323532/1‑63 (MQ=255)
                    ttCATCTTCGTCGATGATGCTCATGGCAAATCCGACGTGTACCAGCACCCACTGGCCCAGTAg                                                     >  1:1227390/1‑63 (MQ=255)
                    ttCATCTTCGTCGATGATGCTCATGGCAAATCCGACGTGTACCAGCACCCACTGGCCCAGTAg                                                     <  1:1451476/63‑1 (MQ=255)
                    ttCATCTTCGTCGATGATGCTCATGGCAAATCCGACGTGTACCAGCACCCACTGGCCCAGTAg                                                     >  1:361274/1‑63 (MQ=255)
                    ttCATCTTCGTCGATGATGCTCATGGCAAATCCGACGTGTACCAGCACCCACTGGCCCAGTAg                                                     >  1:1767798/1‑63 (MQ=255)
                    ttCATCTTCGTCGATGATGCTAATGGCAAATCCGACGTGTACCAGCACCCACTGGCCCAGTAg                                                     <  1:1781644/63‑1 (MQ=255)
                          ttCGTCGATGATGCTCATGGCAAATCCGACGTGTACCAGCAccc                                                                  >  1:2141779/1‑44 (MQ=255)
                          ttCGTCGATGATGCTCATGGCAAATCCGACGTGTACCAGCAccc                                                                  >  1:16005/1‑44 (MQ=255)
                          ttCGTCGATGATGCTCATGGCAAATCCGACGTGTACCAGCAccc                                                                  >  1:2184311/1‑44 (MQ=255)
                          ttCGTCGATGATGCTCATGGCAAATCCGACGTGTACCAGCAccc                                                                  >  1:361782/1‑44 (MQ=255)
                          ttCGTCGATGATGCTCATGGCAAATCCGACGTGTACCAGCAccc                                                                  >  1:2206178/1‑44 (MQ=255)
                          ttCGTCGATGATGCTCATGGCAAATCCGACGTGTACCAGCAccc                                                                  >  1:518190/1‑44 (MQ=255)
                          ttCGTCGATGATGCTCATGGCAAATCCGACGTGTACCAGCAccc                                                                  >  1:588465/1‑44 (MQ=255)
                          ttCGTCGATGATGCTCATGGCAAATCCGACGTGTACCAGCAccc                                                                  >  1:2338113/1‑44 (MQ=255)
                          ttCGTCGATGATGCTCATGGCAAATCCGACGTGTACCAGCAccc                                                                  >  1:1375576/1‑44 (MQ=255)
                          ttCGTCGATGATGCTCATGGCAAATCCGACGTGTACCAGCAccc                                                                  >  1:3010583/1‑44 (MQ=255)
                               cgATGATGCTCATGGCAAATCCGACGTGTACCAGCACCCACTGGCCCAGTAg                                                     <  1:723996/52‑1 (MQ=255)
                                         cATGGCAAATCCGACGTGTACCAGCACCCACTGGCCCAGTAGATCGGCAGGGTTACCTTCACAAATCa                           <  1:812984/68‑1 (MQ=255)
                                         cATGGCAAATCCGACGTGTACCAGCACCCACTGGCCCAGTAGATCGGCAGGGTTACCTTCACAAATCa                           <  1:3135624/68‑1 (MQ=255)
                                         cATGGCAAATACGACGTGTACCAGCACCCACTGGCCCAGTAGATCGGCAGGGTTACCTTCACAAATCa                           <  1:2287120/68‑1 (MQ=255)
                                                                gCACCCACTGGCCCAGTAGATCGGCAGGGTTACCTTCACAAATCAGGGCGATATTCACATCGCGCTTGa   <  1:998917/69‑1 (MQ=255)
                                                                gCACCCACTGGCCCAGTAGATCGGCAGGGTTACCTTCACAAATCAGGGCGATATTCACATCGCGCTTGa   <  1:1030560/69‑1 (MQ=255)
                                                                gCACCCACTGGCCCAGTAGATCGGCAGGGTTACCTTCACAAATCAGGGCGATATTCACATCGCGCTTGa   <  1:3374041/69‑1 (MQ=255)
                                                                gCACCCACTGGCCCAGTAGATCGGCAGGGTTACCTTCACAAATCAGGGCGATATTCACATCGCGCTTGa   <  1:2985598/69‑1 (MQ=255)
                                                                gCACCCACTGGCCCAGTAGATCGGCAGGGTTACCTTCACAAATCAGGGCGATATTCACATCGCGCTTGa   <  1:1835443/69‑1 (MQ=255)
                                                                gCACCCACTGGCCCAGTAGATCGGCAGGGTTACCTTCACAAATCAGGGCGATATTCACATCGCGCTTGa   <  1:107764/69‑1 (MQ=255)
                                                                 cACCCACTGGCCCAGTAGATCGGCAGGGTTACCTTCACAAATCAGGGCGATATTCACATCGCGCTTGAt  <  1:340269/69‑1 (MQ=255)
                                                                 cACCCACTGGCCCAGTAGATCGGCAGGGTTACCTTCACAAATCAGGGCGATATTCACATCGCGCTTGAt  <  1:2733101/69‑1 (MQ=255)
                                                                 cACCCACTGGCCCAGTAGATCGGCAGGGTTACCTTCACAAATCAGGGCGATATTCACATCGCGCTTGAt  <  1:1406846/69‑1 (MQ=255)
                                                                 cACCCACTGGCCCAGTAGATCGGCAGGGTTACCTTCAAAAATCAGGGCGATATTCACATCGCGCTTGAt  <  1:1365199/69‑1 (MQ=255)
                                                                 |                                                                    
GCGTCTAATGTGGCTTTGGCTTCATCTTCGTCGATGATGCTCATGGCAAATCCGACGTGTACCAGCACCCACTGGCCCAGTAGATCGGCAGGGTTACCTTCACAAATCAGGGCGATATTCACATCGCGCTTGAT  >  minE/2002513‑2002646

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