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 F3 I0 R2 232 76.3 4135488 90.9% 3759158 60.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,890,961 G→A 25.8% P208S (CCG→TCG)  gudP ← predicted D‑glucarate transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,890,9610GA25.8% 118.2 / 43.8 66P208S (CCG→TCG) gudPpredicted D‑glucarate transporter
Reads supporting (aligned to +/- strand):  ref base G (23/26);  new base A (9/8);  total (32/34)
Fisher's exact test for biased strand distribution p-value = 7.81e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.59e-01

TTGCTGATCCATATTGATCAGCGCACCACCCGCGGCGATGTACTCCAGCTCTTTCTTATTTACCCCCGGATGTTGATTTGGCTCGTGGATGACTTTCAACCAGATAAAGCTGATGACAATCCCCA  >  minE/1890893‑1891017
                                                                    |                                                        
ttGCTGATCCATATTGATCAGCGCACCACCCGCGGCGATGTACTCCAGCTCTTTCTTATTTACCCCCGGAt                                                        >  1:3654781/1‑71 (MQ=255)
   cTGATCCATATTGATCAGCGCACCACCCGCGGCGATGTACTCCAGCTCTTTCTTATTTACCCCCGAATGtt                                                     <  1:1267094/71‑1 (MQ=255)
        ccATATTGATCAGCGCACCACCCGCGGCGATGTACTCCAGCTCTTTCTTATTTACCCCCGGAt                                                        >  1:2623727/1‑63 (MQ=255)
        ccATATTGATCAGCGCACCACCCGCGGCGATGTACTCCAGCTCTTTCTTATTTACCCCCGGAt                                                        >  1:3560322/1‑63 (MQ=255)
           tatTGATCAGCGCACCACCCGCGGCGATGTACTCCAGCTCTTTCTTATTTACCCCCGGATGTTGAttt                                                <  1:987542/68‑1 (MQ=255)
           tatTGATCAGCGCACCACCCGCGGCGATGTACTCCAGCTCTTTCTTATTTACCCCCGGATGTTGAttt                                                <  1:313491/68‑1 (MQ=255)
           tatTGATCAGCGCACCACCCGCGGCGATGTACTCCAGCTCTTTCTTATTTACCCCCGGATGTTGAttt                                                <  1:1823626/68‑1 (MQ=255)
           tatTGATCAGCGCACCACCCGCGGCGATGTACTCCAGCTCTTTCTTATTTACCCCCGGATGTTGAttt                                                <  1:1524278/68‑1 (MQ=255)
           tatTGATCAGCGCACCACCCGCGGCGATGTACTCCAGCTCTTTCTTATTTACCCCCGGATGTTGAttt                                                <  1:3658177/68‑1 (MQ=255)
             ttGATCAGCGCACCACCCGCGGCGATGTACTCCAGCTCTTTCTTATTTACCCCCgg                                                          >  1:2119766/1‑56 (MQ=255)
             ttGATCAGCGCACCACCCGCGGCGATGTACTCCAGCTCTTTCTTATTTACCCCCGGATGTTGATTTgg                                              >  1:1663571/1‑68 (MQ=255)
             ttGATCAGCGCACCACCCGCGGCGATGTACTCCAGCTCTTTCTTATTTACCCCCGGATGTTGATTTgg                                              >  1:752009/1‑68 (MQ=255)
             ttGATCAGCGCACCACCCGCGGCGATGTACTCCAGCTCTTTCTTATTTACCCCCGGATGTTGATTTgg                                              >  1:3022120/1‑68 (MQ=255)
             ttGATCAGCGCACCACCCGCGGCGATGTACTCCAGCTCTTTCTTATTTACCCCCGGATGTTGATTTgg                                              >  1:2951804/1‑68 (MQ=255)
             ttGATCAGCGCACCACCCGCGGCGATGTACTCCAGCTCTTTCTTATTTACCCCCGGATGTTGATTTGGCTc                                           >  1:1624386/1‑71 (MQ=255)
             ttGATCAGCGCACCACCCGCGGCGATGTACTACAGCTCTTTCTTATTTACCCCCGAATGTTGATTTGGCTc                                           >  1:837092/1‑71 (MQ=255)
               gATCAGCGCACCACCCGCGGCGATGTACTCCAGCTCTTTCTTATTTACCCCCGAATGTTGATTTGGCTCg                                          <  1:772343/70‑1 (MQ=255)
               gATCAGCGCACCACCCGCGGCGATGTACTCCAGCTCTTTCTTATTTACCCCCGAATGTTGATTTGGCTCg                                          <  1:3329567/70‑1 (MQ=255)
               gATCAGCGCACCACCCGCGGCGATGTACTCCAGCTCTTTCTTATTTACCCCCGAATGTTGATTTGGCTCg                                          <  1:3061182/70‑1 (MQ=255)
                 tCAGCGCACCACCCGCGGCGATGTACTCCAGCTCTTTCTTATTTACCCCCGGATGTTGATTTGGCTCGTg                                        <  1:730644/70‑1 (MQ=255)
                      gcACCACCCGCGGCGATGTACTCCAGCTCTTTCTTATTTACCCCCGGATGTTGATCTGGCTCGTGGATGAc                                  <  1:2430042/71‑1 (MQ=255)
                       caccacCCGCGGCGATGTACTCCAGCTCTTTCTTATTTACCCCCGGATGTTGATTTGGCTCGTGGATGAc                                  <  1:1911656/70‑1 (MQ=255)
                         ccaccCGCGGCGATGTACTCCAGCTCTTTCTTATTTACCCCCGGATGTTGAtt                                                 >  1:550824/1‑53 (MQ=255)
                         ccaccCGCGGCGATGTACTCCAGCTCTTTCTTATTTACCCCCGGATGTTGAt                                                  >  1:3880815/1‑52 (MQ=255)
                         caaccCGCGGCGATGTACTCCAGCTCTTTCTTATTTACCCCCGGATGTTGAtt                                                 >  1:135551/3‑53 (MQ=255)
                          caccCGCGGCGATGTACTCCAGCTCTTTCTTATTTACCCCCGGATGTTGATTTGGCTCGTGGATGACTTTc                              <  1:2598211/71‑1 (MQ=255)
                          caccCGCGGCGATGTACTCCAGCTCTTTCTTATTTACCCCCGGATGTTGATTTGGCTCGTGGATGACTTTc                              <  1:718554/71‑1 (MQ=255)
                          caccCGCGGCGATGTACTCCAGCTCTTTCTTATTTACCCCCGGATGTTGATTTGGCTCGTGGATGACTTTc                              <  1:2673363/71‑1 (MQ=255)
                          caccCGCGGCGATGTACTCCAGCTCTTTCTTATTTACCCCCGGATGTTGATTTGGCTCGTGGATGACTTTc                              <  1:921845/71‑1 (MQ=255)
                           accCGCGGCGATGTACTCCAGCTCTTTCTTATTTACCCCCGGATGTTGATTTGGCTCGTGGATGACTTTc                              <  1:657602/70‑1 (MQ=255)
                              cgcgGCGATGTACTCCAGCTCTTTCTTATTTACCCCCGGATGTTGATTTGGCTCGTGGATGACTTTGAAc                           >  1:3520918/1‑70 (MQ=255)
                              cgcgGCGATGTACTCCAGCTCTTTCTTATTTACCCCCGGATGTTGATTTGGCTCGTGGATGACTTTCAAcc                          <  1:2996622/71‑1 (MQ=255)
                              cgcgGCGATGTACTCCAGCTCTTTCTTATTTACCCCCGGATGTTGATTTGGCTCGTGGATGACTTTCAAcc                          <  1:2241381/71‑1 (MQ=255)
                                    gATGTACTCCAGCTCTTTCTTATTTACCCCCGGATGTTGATTTGGCTCGTGGATGACTTTCAACCAGATa                     >  1:2916633/1‑70 (MQ=255)
                                    gATGTACTCCAGCTCTTTCTTATTTACCCCCGGATGTTGATTTGGCTCGTGGATGACTTTCAACCAGATa                     >  1:815242/1‑70 (MQ=255)
                                    gATGTACTCCAGCTCTTTCTTATTTACCCCCGGATGTTGATTTGGCTAGTGGATGACTTTCAACCAGATa                     >  1:3315019/1‑70 (MQ=255)
                                    gATGTACTCCAGCTCTTTCTTATTTACCCCCGAATGTTGATTTGGCTCGTGGATGACTTTCAACCAGATaa                    <  1:40370/71‑1 (MQ=255)
                                    gATGTACTCCAGCTCTTTCTTATTTACCCCCGAATGTTGATTTGGCTCGTGGATGACTTTCAACCAGATaa                    <  1:1194570/71‑1 (MQ=255)
                                    gATGTACTCCAGCTCTTTCTTATTTACCCCCGAATGTTGATTTGGCTCGTGGATGACTTTCAACCAGATa                     >  1:3312670/1‑70 (MQ=255)
                                    gATGTACTCCAGCTCTTTCTTATTTACCCCCGAATGTTGATTTGGCTCGTGGATGACTTTCAACCAGATa                     >  1:2262301/1‑70 (MQ=255)
                                    gATGTACTCCAGCTCTTTCTTATTTACCCCCGAATGTTGATTTGGCTCGTGGATGACTTTCAACCAGATa                     >  1:3726614/1‑70 (MQ=255)
                                        tACTCCAGCTCTTTCTTATTTACCCCCGGATGTTGATTTGGCTCGTGGATGACTTTCAACCAGATAAAGCt                <  1:3917611/71‑1 (MQ=255)
                                             cAGCTCTTTCTTATTTACCCCTGGATGTTGATTTGGCTCGTGGATGACTTTCAACCAGATAAAGCtga              >  1:3269352/1‑68 (MQ=255)
                                             cAGCTCTTTCTTATTTACCCCCGGATGTTGATTTGGCTCGTGGa                                      >  1:1020842/1‑44 (MQ=255)
                                              aGCTCTTTCTTATTTACCCCCGGATGTTGATTTGGCTCGTGGATGACTTTCAACCAGATAAAGCTGATGAc          <  1:1898311/71‑1 (MQ=255)
                                               gCTCTTTCTTATTTACCCCCGGATGTTGATTTGGCTCGTGGATGACTTTCAACCAGATAAAGCTGATGACa         <  1:3653140/71‑1 (MQ=255)
                                               gCTCTTTCTTATTTACCCCCGGATGTTGATTTGGCTCGTGGATGACTTTCAACCAGATAAAGCTGATGACa         <  1:3657912/71‑1 (MQ=255)
                                               gCTCTTTCTTATTTACCCCCGAATGTTGATTTGGCTCGTGGATGACTTTCAACCAGATAAAGCtga              >  1:3681444/1‑66 (MQ=255)
                                               gCTCTTTCTTATTTACCCCCGAATGTTGATTTGGCTCGTGGATGACTTTCAACCAGATAAAGCTGATGAc          <  1:2731955/70‑1 (MQ=255)
                                                ctctTTCTTATTTACCCCCGGATGTTGATTTGGCTCGTGGATGACTTTCAACCAGATAAAGCTGCTGACaa        <  1:532086/71‑1 (MQ=255)
                                                ctctTTCTTATTTACCCCCGGATGTTGATTTGGCTCGTGGATGACTTTCAACCAGATAAAGCTGATGACa         <  1:2852442/70‑1 (MQ=255)
                                                  ctttcttATTTACCCCCGAATGTTGATTTGGCTCGTg                                        <  1:2489328/37‑1 (MQ=255)
                                                    ttcttATTTACCCCCGAATGTTGATTTGGCTCGTGGa                                      >  1:95728/1‑37 (MQ=255)
                                                    ttcttATTTACCCCCGAATGTTGATTTGGCTCGTGGa                                      >  1:3366295/1‑37 (MQ=255)
                                                    ttcttATTTACCCCCGAATGTTGATTTGGCTCGTGGa                                      >  1:2455962/1‑37 (MQ=255)
                                                     tcttATTTACCCCCGGATGTTGATTTGGCTCGTGGATGACTTTCAACCAGATAAAGCTGATGACAAt       >  1:1096032/1‑67 (MQ=255)
                                                     tcttATTTACCCCCGGATGTTGATTTGGCTCGTGGATGACTTTCAACCAGATAAAGCTGATGACAAt       >  1:3026430/1‑67 (MQ=255)
                                                     tcttATTTACCCCCGGATGTTGATTTGGCTCGTGGATGACTTTCAACCAGATAAAGCTGATGACAAt       >  1:3220461/1‑67 (MQ=255)
                                                      cttATTTACCCCCGAATGTTGATTTGGCTCGTGGATGACTTTCAACCAGATAAAGCTGATGACAATcca    >  1:460984/1‑68 (MQ=255)
                                                         aTTTACCCCCGGATGTTGATTTGGCTCGTGGATGACTTTCAACCAGATAAAg                  >  1:2975778/1‑52 (MQ=255)
                                                         aTTTACCCCCGGATGTTGATTTGGCTCGTGGATGACTTTCAACCAGATAAAg                  >  1:1220642/1‑52 (MQ=255)
                                                         aTTTACCCCCGGATGTTGATTTGGCTCGTGGATGACTTTCAACCAGATAAAg                  >  1:1218891/1‑52 (MQ=255)
                                                         aTTTACCCCCGGATGTTGATTTGGCTCGTGGATGACTTTCAACCAGATAAAGCTGATGACAATCCCCa  <  1:2745727/68‑1 (MQ=255)
                                                          tttACCCCCGGATGTTGATTTGGCTCGTGGATGACTTTCAACCAGATAAAGCTGATGACAATCCCCa  <  1:177006/67‑1 (MQ=255)
                                                             aCCCCCGGATGTTGATTTGGCTCGTGGATGACTTTCAACCa                         <  1:2972119/41‑1 (MQ=255)
                                                             aCCCCCGGATGTTGATTTGGCTCGTGGATGACTTTCAACCa                         <  1:46522/41‑1 (MQ=255)
                                                             aCCCCCGGATGTTGATTTGGCTCGTGGATGACTTTCAACCa                         <  1:3911498/41‑1 (MQ=255)
                                                                    |                                                        
TTGCTGATCCATATTGATCAGCGCACCACCCGCGGCGATGTACTCCAGCTCTTTCTTATTTACCCCCGGATGTTGATTTGGCTCGTGGATGACTTTCAACCAGATAAAGCTGATGACAATCCCCA  >  minE/1890893‑1891017

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