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 2,228,311 T→G 46.2% V105V (GTT→GTG)  yhdZ → predicted amino‑acid transporter subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,228,3110TG46.2% 0.3 / 107.3 91V105V (GTT→GTG) yhdZpredicted amino‑acid transporter subunit
Reads supporting (aligned to +/- strand):  ref base T (33/16);  new base G (21/21);  total (54/37)
Fisher's exact test for biased strand distribution p-value = 1.34e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.87e-01

CAGGCAGGAAGTGGGAATGGTCTTTCAGCATTTCAATCTCTTCCCTCATCTGACCGTTTTACAGAACTGTACCCTGGCACCGATTTGGGTACGCAAGATGCCTAAGAAAGAGGCTGAAGATCTG  >  minE/2228254‑2228377
                                                         |                                                                  
caggcaggAAGTGGGAATGGTCTTTCAGCATTTCAATCTCTTCCCTCATCTGACCGTTTTACAGAACTg                                                         <  1:940760/69‑1 (MQ=255)
caggcaggAAGTGGGAATGGTCTTTCAGCATTTCAATCTCTTCCCTCATCTGACCGTTTTACAGAACTg                                                         <  1:1141058/69‑1 (MQ=255)
caggcaggAAGTGGGAATGGTCTTTCAGCATTTCAATCTCTTCCCTCATCTGACCGTTTTACAGAACTg                                                         <  1:2457881/69‑1 (MQ=255)
caggcaggAAGTGGGAATGGTCTTTCAGCATTTCAATCTCTTCCCTCATCTGACCGTTTTACAGAACTg                                                         <  1:1006261/69‑1 (MQ=255)
caggcaggAAGTGGGAATGGTCTTTCAGCATTTCAATCTCTTCCCTCATCTGACCGTTTTACAGAACTg                                                         <  1:867695/69‑1 (MQ=255)
 aggcaggAAGTGGGAATGGTCTTTCAGCATTTCAATCTCTTCCCTCATCTGACCGTTTTACAGAACTg                                                         <  1:224948/68‑1 (MQ=255)
 aggcaggAAGTGGGAATGGTCTTTCAGCATTTCAATCTCTTCCCTCATCTGACCGTTTTACAGAACTg                                                         <  1:286092/68‑1 (MQ=255)
   gcaggAAGTGGGAATGGTCTTTCAGCATTTCAATCTCTTCCCTCATCTGACCGTTTTACAGAACTGTa                                                       <  1:1523424/68‑1 (MQ=255)
   gcaggAAGTGGGAATGGTCTTTCAGCATTTCAATCTCTTCCCTCATCTGACCGTTTTACAGAACTGTa                                                       <  1:2772068/68‑1 (MQ=255)
   gcaggAAGTGGGAATGGTCTTTCAGCATTTCAATCTCTTCCCTCATCTGACCGTTTTACAGAACTGTa                                                       <  1:1312800/68‑1 (MQ=255)
   gcaggAAGTGGGAATGGTCTTTCAGCATTTCAATCTCTTCCCTCATCTGACCGTTTTACAGAACTGTa                                                       <  1:3233007/68‑1 (MQ=255)
                 tGGTCTTTCAGCATTTCAATCTCTTGCCTCATCTGACCGTGTTGCAGAACTGTACCCt                                                   <  1:1312922/58‑1 (MQ=255)
                 tGGTCTTTCAGCATTTCAATCTCTTCCCTCATCTGACCGTGTTGCAGAAc                                                           >  1:3188751/1‑50 (MQ=39)
                 tGGTCTTTCAGCATTTCAATCTCTTCCCTCATCTGACCGTGTTGCAGAAc                                                           >  1:3353534/1‑50 (MQ=39)
                 tGGTCTTTCAGCATTTCAATCTCTTCCCTCATCTGACCGTGTTGCAGAAc                                                           >  1:3289174/1‑50 (MQ=39)
                 tGGTCTTTCAGCATTTCAATCTCTTCCCTCATCTGACCGTGTTGCAGAAc                                                           >  1:195694/1‑50 (MQ=39)
                 tGGTCTTTCAGCATTTCAATCTCTTCCCTCATCTGACCGTGTTGCAGAAc                                                           >  1:511904/1‑50 (MQ=39)
                 tGGTCTTTCAGCATTTCAATCTCTTCCCTCATCTGACCGTGTTGCAGAAc                                                           >  1:2875144/1‑50 (MQ=39)
                 tGGTCTTTCAGCATTTCAATCTCTTCCCTCATCTGACCGTGTTGCAGAAc                                                           >  1:1982149/1‑50 (MQ=39)
                 tGGTCTTTCAGCATTTCAATCTCTTCCCTCATCTGACCGTGTTGCAGAAc                                                           >  1:2864971/1‑50 (MQ=39)
                 tGGTCTTTCAGCATTTCAATCTCTTCCCTCATCTGACCGTGTTGCAGAAc                                                           >  1:2210658/1‑50 (MQ=39)
                 tGGTCTTTCAGCATTTCAATCTCTTCCCTCATCTGACCGTGTTGCAGAAc                                                           >  1:253804/1‑50 (MQ=39)
                 tGGTCTTTCAGCATTTCAATCTCTTCCCTCATCTGACCGTGTTGCAGAAc                                                           >  1:2431135/1‑50 (MQ=39)
                 tGGTCTTTCAGCATTTCAATCTCTTCCCTCATCTGACCGTGTTGCAGAAc                                                           >  1:789329/1‑50 (MQ=39)
                 tGGTCTTTCAGCATTTCAATCTCTTCCCTCATCTGACCGTGTTGCAGAAc                                                           >  1:1119568/1‑50 (MQ=39)
                 tGGTCTTTCAGCATTTCAATCTCTTCCCTCATCTGACCGTGTTGCAGAAc                                                           >  1:940258/1‑50 (MQ=39)
                 tGGTCTTTCAGCATTTCAATCTCTTCCCTCATCTGACCGTGTTGCAGAAc                                                           >  1:905731/1‑50 (MQ=39)
                 tGGTCTTTCAGCATTTCAATCTCTTCCCTCATCTGACCGTGTTGCAGAAc                                                           >  1:727644/1‑50 (MQ=39)
                 tGGTCTTTCAGCATTTCAATCTCTTCCCTCATCTGACCGTGTTGCAGAAc                                                           >  1:608905/1‑50 (MQ=39)
                 tGGTCTTTCAGCATTTCAATCTCTTCCCTCATCTGACCGTGTTGCAGAAc                                                           >  1:585570/1‑50 (MQ=39)
                 tGGTCTTTCAGCATTTCAATCTCTTCCCTCATCTGACCGTGTTGCAGAAc                                                           >  1:533484/1‑50 (MQ=39)
                 tGGTCTTTCAGCATTTCAATCTCTTCCCTCATCTGACCGTGTTGCAGAAc                                                           >  1:46701/1‑50 (MQ=39)
                 tGGTCTTTCAGCATTTCAATCTCTTCCCTCATCTGACCGTGTTGCAGAAc                                                           >  1:461397/1‑50 (MQ=39)
                 tGGTCTTTCAGCATTTCAATCTCTTCCCTCATCTGACCGTGTTGCAGAACTGTACCCt                                                   <  1:561957/58‑1 (MQ=255)
                 tGGTCTTTCAGCATTTCAATCTCTTCCCTCATCTGACCGTGTTGCAGAACTGTACCCt                                                   <  1:3361791/58‑1 (MQ=255)
                 tGGTCTTTCAGCATTTCAATCTCTTCCCTCATCTGACCGTGTTGCAGAACTGTACCCt                                                   <  1:808826/58‑1 (MQ=255)
                 tGGTCTTTCAGCATTTCAATCTCTTCCCTCATCTGACCGTGTTGCAGAACTGTACCCt                                                   <  1:891791/58‑1 (MQ=255)
                 tGGTCTTTCAGCATTTCAATCTCTTCCCTCATCTGACCGTGTTGCAGAACTGTACCCt                                                   <  1:903068/58‑1 (MQ=255)
                 tGGTCTTTCAGCATTTCAATCTCTTCCCTCATCTGACCGTGTTGCAGAACTGTACCCt                                                   <  1:2573890/58‑1 (MQ=255)
                 tGGTCTTTCAGCATTTCAATCTCTTCCCTCATCTGACCGTGTTGCAGAACTGTACCCt                                                   <  1:930498/58‑1 (MQ=255)
                 tGGTCTTTCAGCATTTCAATCTCTTCCCTCATCTGACCGTGTTGCAGAACTGTACCCt                                                   <  1:2526380/58‑1 (MQ=255)
                 tGGTCTTTCAGCATTTCAATCTCTTCCCTCATCTGACCGTGTTGCAGAACTGTACCCt                                                   <  1:1968195/58‑1 (MQ=255)
                 tGGTCTTTCAGCATTTCAATCTCTTCCCTCATCTGACCGTGTTGCAGAACTGTACCCt                                                   <  1:1364360/58‑1 (MQ=255)
                 tGGTCTTTCAGCATTTCAATCTCTTCCCTCATCTGACCGTGTTGCAGAACTGTACCCt                                                   <  1:1404609/58‑1 (MQ=255)
                 tGGTCTTTCAGCATTTCAATCTCTTCCCTCATCTGACCGTGTTGCAGAACTGTACCCt                                                   <  1:1425603/58‑1 (MQ=255)
                 tGGTCTTTCAGCATTTCAATCTCTTCCCTCATCTGACCGTGTTGCAGAACTGTACCCt                                                   <  1:1361616/58‑1 (MQ=255)
                 tGGTCTTTCAGCATTTCAATCTCTTCCCTCATCTGACCGTGTTGCAGAACTGTACCCt                                                   <  1:1257584/58‑1 (MQ=255)
                 tGGTCTTTCAGCATTTCAATCTCTTCCCTCATCTGACCGTGTTGCAGAACTGTACCCt                                                   <  1:137658/58‑1 (MQ=255)
                 tGGTCTTTCAGCATTTCAATCTCTTCCCTCATCTGACCGTGTTGCAGAACTGTACCCt                                                   <  1:1215792/58‑1 (MQ=255)
                 tGGTCTTTCAGCATTTCAATCTCTTCCCTCATCTGACCGTGTTGCAGAACTGTACCCt                                                   <  1:222793/58‑1 (MQ=255)
                 tGGTCTTTCAGCATTTCAATCTCTTCCCTCATCTGACCGTGTTGCAGAACTGTACCCt                                                   <  1:2341450/58‑1 (MQ=255)
                 tGGTCTTTCAGCATTTCAATCTCTTCCCTCATCTGACCGTGTTGCAGAACTGTACCCt                                                   <  1:1162825/58‑1 (MQ=255)
                   gTCTTTCAGCATTTCAATCTCTTCCCTCATCTGACCGTTTTACAGAACTGTACCCTGGCACCGATTTg                                       >  1:1935106/1‑68 (MQ=255)
                   gTCTTTCAGCATTTCAATCTCTTCCCTCATCTGACCGTTTTACAGAACTGTACCCTGGCACCGATTTg                                       >  1:1245779/1‑68 (MQ=255)
                          aGCATTTCAATCTCTTCCCTCATCTGACCGTGTTGCAGAACTGTACCCt                                                   <  1:45147/49‑1 (MQ=38)
                            cATTTCAATCTCTTCCCTCATCTGACCGTTTTACAGAACTGTACCCTGGCACCGATTTGGGTACGCaa                              <  1:1169758/68‑1 (MQ=255)
                            cATTTCAATCTCTTCCCTCATCTGACCGTTTTACAGAACTGTACCCTGGCACCGATTTGGGTACGCaa                              <  1:738226/68‑1 (MQ=255)
                                tCAATCTCTTACCTCATCTGACCGTTTTACAGAACTGTa                                                       >  1:918194/1‑39 (MQ=255)
                                    tctcTTCCCTCATCTGACCGTTTTACAGAACTGTACCCTGGCACCGATTTGGGTa                                   >  1:1695351/1‑55 (MQ=255)
                                    tctcTTCCCTCATCTGACCGTTTTACAGAACTGTACCCTGGCACCGATTTGGGTACGCAAGATGCCTa                      >  1:2441862/1‑68 (MQ=255)
                                    tctcTTCCCTCATCTGACCGTTTTACAGAACTGTACCCTGGCACCGATTTGGGTACGCAAGATGCCTa                      >  1:2775423/1‑68 (MQ=255)
                                    tctcTTCCCTCATCTGACCGTTTTACAGAACTGTACCCTGGCACCGATTTGGGTACGCAAGATGCCTa                      >  1:485890/1‑68 (MQ=255)
                                    tctcTTCCCTCATCTGACCGTTTTACAGAACTGTACCCTGGCACCGATTTGGGTACGCAAGATGCCTa                      >  1:3376214/1‑68 (MQ=255)
                                    tctcTTCCCTCATCTGACCGTTTTACAGAACTGTACCCTGGCACCGATTTGGGTACGCAAGATGCCTa                      >  1:336075/1‑68 (MQ=255)
                                    tctcTTCCCTCATCTGACCGTTTTACAGAACTGTACCCTGGCACCGATTTGGGTACGCAAGATGCCTa                      >  1:3158301/1‑68 (MQ=255)
                                     ctctTCCCTCATCTGCCCGTTTTACAGAACTGTACCCTGGCACCGATTTGGGTACGCa                               >  1:2307064/1‑58 (MQ=255)
                                     ctctTCCCTCATCTGACCGTTTTACAGAACTGTACCCTGGCACCGATTTGGGTACGCa                               >  1:1943257/1‑58 (MQ=255)
                                     ctctTCCCTCATCTGACCGTTTTACAGAACTGTACCCTGGCACCGATTTGGGTACGCa                               >  1:3295644/1‑58 (MQ=255)
                                     ctctTCCCTCATCTGACCGTTTTACAGAACTGTACCCTGGCACCGATTTGGGTACGCa                               >  1:3229696/1‑58 (MQ=255)
                                     ctctTCCCTCATCTGACCGTTTTACAGAACTGTACCCTGGCACCGATTTGGGTACGCa                               >  1:1968717/1‑58 (MQ=255)
                                     ctctTCCCTCATCTGACCGTTTTACAGAACTGTACCCTGGCACCGATTTGGGTACGCa                               >  1:493372/1‑58 (MQ=255)
                                     ctctTCCCTCATCTGACCGTTTTACAGAACTGTACCCTGGCACCGATTTGGGTACGCa                               >  1:3109694/1‑58 (MQ=255)
                                     ctctTCCCTCATCTGACCGTTTTACAGAACTGTACCCTGGCACCGATTTGGGTACGCa                               >  1:2554986/1‑58 (MQ=255)
                                     ctctTCCCTCATCTGACCGTTTTACAGAACTGTACCCTGGCACCGATTTGGGTACGCa                               >  1:144253/1‑58 (MQ=255)
                                     ctctTCCCTCATCTGACCGTTTTACAGAACTGTACCCTGGCACCGATTTGGGTACGCa                               >  1:2984072/1‑58 (MQ=255)
                                     ctctTCCCTCATCTGACCGTTTTACAGAACTGTACCCTGGCACCGATTTGGGTACGCa                               >  1:1132157/1‑58 (MQ=255)
                                     ctctTCCCTCATCTGACCGTTTTACAGAACTGTACCCTGGCACCGATTTGGGTACGCa                               >  1:2945362/1‑58 (MQ=255)
                                     ctctTCCCTCATCTGACCGTTTTACAGAACTGTACCCTGGCACCGATTTGGGTACGCa                               >  1:1969744/1‑58 (MQ=255)
                                     ctctTCCCTCATCTGACCGTTTTACAGAACTGTACCCTGGCACCGATTTGGGTACGCAAGATGCCTaa                     >  1:800257/1‑68 (MQ=255)
                                              cATCTGACCGTTTTACAAAACTGTACCCTGGCACCGATTTGGGTACGCaa                              <  1:1962466/50‑1 (MQ=255)
                                                  tGACCGTTTTACAGAACTGTACCCTGGCACCGATTTGGGTACGCAAGATGCCTAAGAAAGAgg             >  1:682746/1‑63 (MQ=255)
                                                  tGACCGTTTTACAGAACTGTACCCTGGCACCGATTTGGGTACGCAAGATGCCTAAGAAAGAGGc            >  1:95341/1‑64 (MQ=255)
                                                  tGACCGTTTTACAGAACTGTACCCTGGCACCGATTTGGGTACGCAAGATGCCTAAGAAAGAGGc            >  1:1386983/1‑64 (MQ=255)
                                                  tGACCGTTTTACAGAACTGTACCCTGGCACCGATTTGGGTACGCAAGATGCCTAAGAAAGAGGc            >  1:1936502/1‑64 (MQ=255)
                                                  tGACCGTTTTACAGAACTGTACCCTGGCACCGATTTGGGTACGCAAGATGCCTAAGAAAGAGGc            >  1:2089788/1‑64 (MQ=255)
                                                  tGACCGTTTTACAGAACTGTACCCTGGCACCGATTTGGGTACGCAAGATGCCTAAGAAAGAGGc            >  1:2284956/1‑64 (MQ=255)
                                                  tGACCGTTTTACAGAACTGTACCCTGGCACCGATTTGGGTACGCAAGATGCCTAAGAAAGAGGc            >  1:2730974/1‑64 (MQ=255)
                                                  tGACCGTTTTACAGAACTGTACCCTGGCACCGATTTGGGTACGCAAGATGCCTAAGAAAGAGGc            >  1:2341564/1‑64 (MQ=255)
                                                  tGACAGTTTTACAGAACTGTACCCTGGCACCGATTTGGGTACGCAAGATGCCTaagaaaga               >  1:1688980/1‑61 (MQ=255)
                                                       gTTTTACAGAACTGTACCCTGGCACCGATTTGGGTACGCAAGATGCCTAAGAAAGAGGCTGAAGATCTg  <  1:1845244/69‑1 (MQ=255)
                                                       gTTTTACAGAACTGTACCCTGGCACCGATTTGGGTACGCAAGATGCCTAAGAAAGAGGCTGAAGATCTg  <  1:2647626/69‑1 (MQ=255)
                                                        ttttACAGAACTGTACCCTGGCACCGATTTGGGTACGCAAGATGCCTAAGAAAGAGGCTGAAGATCTg  <  1:2347472/68‑1 (MQ=255)
                                                         |                                                                  
CAGGCAGGAAGTGGGAATGGTCTTTCAGCATTTCAATCTCTTCCCTCATCTGACCGTTTTACAGAACTGTACCCTGGCACCGATTTGGGTACGCAAGATGCCTAAGAAAGAGGCTGAAGATCTG  >  minE/2228254‑2228377

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