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 2,885,111 T→C 28.1% I105I (ATT→ATC)  cysQ → PAPS (adenosine 3'‑phosphate 5'‑phosphosulfate) 3'(2'),5'‑bisphosphate nucleotidase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,885,1110TC28.1% 120.6 / 51.5 117I105I (ATT→ATC) cysQPAPS (adenosine 3'‑phosphate 5'‑phosphosulfate) 3'(2'),5'‑bisphosphate nucleotidase
Reads supporting (aligned to +/- strand):  ref base T (24/60);  new base C (21/12);  total (45/72)
Fisher's exact test for biased strand distribution p-value = 6.72e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.73e-01

Only 100 of 119 total aligned reads displayed.

GACCCGCTGGATGGTACTAAAGAGTTTATTAAACGTAATGGCGAATTCACCGTTAACATTGCGCTCATTGACCATGGCAAACCGATTTTAGGCGTGGTGTATGCGCCGGTAATGAACGTAATGTACAGCGCGGCAG  >  minE/2885043‑2885178
                                                                    |                                                                   
gACCCGCTGGATGGTACTAAAGAGTTTATTAAACGTAATGGCGAATTCACCGTTAACATTGCGCTCAtt                                                                     >  1:66001/1‑69 (MQ=255)
   ccGCTGGATGGTACTAAAGAGTTTATTAAACGTAATGGCGAATTCACCGTTAACATTGAGCTCATTGAc                                                                  <  1:707088/69‑1 (MQ=255)
                cTAAAGAGTTTATTAAACGTAATGGCGAATTCACCGTTAACATTGCGCTCATCGACCacg                                                              >  1:1302380/1‑58 (MQ=255)
                cTAAAGAGTTTATTAAACGTAATGGCGAATTCACCGTTAACATTGCGCTCATCGACCacg                                                              >  1:17741/1‑58 (MQ=255)
                cTAAAGAGTTTATTAAACGTAATGGCGAATTCACCGTTAACATTGCGCTCATCGACCacg                                                              >  1:2612437/1‑58 (MQ=255)
                cTAAAGAGTTTATTAAACGTAATGGCGAATTCACCGTTAACATTGCGCTCATCGACCacg                                                              >  1:2630701/1‑58 (MQ=255)
                cTAAAGAGTTTATTAAACGTAATGGCGAATTCACCGTTAACATTGCGCTCATCGACCacg                                                              >  1:1450296/1‑58 (MQ=255)
                cTAAAGAGTTTATTAAACGTAATGGCGAATTCACCGTTAACATTGCGCTCATCGACCacg                                                              >  1:725444/1‑58 (MQ=255)
                cTAAAGAGTTTATTAAACGTAATGGCGAATTCACCGTTAACATTGCGCTCATCGACCacg                                                              >  1:2941442/1‑58 (MQ=255)
                cTAAAGAGTTTATTAAACGTAATGGCGAATTCACCGTTAACATTGCGCTCATCGACCacg                                                              >  1:70688/1‑58 (MQ=255)
                cTAAAGAGTTTATTAAACGTAATGGCGAATTCACCGTTAACATTGCGCTCATCGACCacg                                                              >  1:2968150/1‑58 (MQ=255)
                cTAAAGAGTTTATTAAACGTAATGGCGAATTCACCGTTAACATTGCGCTCATCGACCacg                                                              >  1:1244463/1‑58 (MQ=255)
                cTAAAGAGTTTATTAAACGTAATGGCGAATTCACCGTTAACATTGCGCTCATCGACCacg                                                              >  1:1214613/1‑58 (MQ=255)
                cTAAAGAGTTTATTAAACGTAATGGCGAATTCACCGTTAACATTGCGCTCATCGACCacg                                                              >  1:843387/1‑58 (MQ=255)
                cTAAAGAGTTTATTAAACGTAATGGCGAATTCACCGTTAACATTGCGCTCATCGACCacg                                                              >  1:3050505/1‑58 (MQ=255)
                cTAAAGAGTTTATTAAACGTAATGGCGAATTCACCGTTAACATTGCGCTCATCGACCacg                                                              >  1:1091067/1‑58 (MQ=255)
                cTAAAGAGTTTATTAAACGTAATGGCGAATTCACCGTTAACATTGCGCTCATCGACCacg                                                              >  1:310899/1‑58 (MQ=255)
                cTAAAGAGTTTATTAAACGTAATGGCGAATTCACCGTTAACATTGCGCTCATCGACCacg                                                              >  1:1026171/1‑58 (MQ=255)
                cTAAAGAGTTTATTAAACGTAATGGCGAATTCACCGTTAACATTGCGCTCATCGACCacg                                                              >  1:3350686/1‑58 (MQ=255)
                  aaaGAGTTTATTAAACGTAATGGCGAATTCACCGTTAACATTGCGCTCATTGACCATGGCAAACCg                                                      <  1:1544412/66‑1 (MQ=255)
                  aaaGAGTTTATTAAACGTAATGGCGAATTCACCGTTAACATTGCGCTCATTGACCATGGCAAACCg                                                      <  1:2056996/66‑1 (MQ=255)
                  aaaGAGTTTATTAAACGTAATGGCGAATTCACCGTTAACATTGCGCTCATTGACCATGGCAAACCg                                                      <  1:223080/66‑1 (MQ=255)
                  aaaGAGTTTATTAAACGTAATGGCGAATTCACCGTTAACATTGCGCTCATTGACCATGGCAAACCg                                                      <  1:2420920/66‑1 (MQ=255)
                  aaaGAGTTTATTAAACGTAATGGCGAATTCACCGTTAACATTGCGCTCATTGACCATGGCAAACCg                                                      <  1:440896/66‑1 (MQ=255)
                  aaaGAGTTTATTAAACGTAATGGCGAATTCACCGTTAACATTGCGCTCATTGACCATGGCAAACCg                                                      <  1:2976643/66‑1 (MQ=255)
                   aaGAGTTTATTAAACGTAATGGCGAATTCACCGTTAACATTGCGCTCATTGACCATGGCAAACCGAt                                                    >  1:101183/1‑67 (MQ=255)
                     gagTTTATTAAACGTAATGGCGAATTCACCGTTAACATTGCGCTCATTGACCATGGCAAACCGAtttt                                                 >  1:2224180/1‑68 (MQ=255)
                     gagTTTATTAAACGTAATGGCGAATTCACCGTTAACATTGCGCTCATTGACCATGGCAAACCGAttt                                                  <  1:2513986/67‑1 (MQ=255)
                     gagTTTATTAAACGTAATGGCGAATTCACCGTTAACATTGCGCTCATTGACCATGGCAAACCGAttt                                                  <  1:2593061/67‑1 (MQ=255)
                     gagTTTATTAAACGTAATGGCGAATTCACCGTTAACATTGCGCTCATTGACCATGGCAAACCGAttt                                                  <  1:1786695/67‑1 (MQ=255)
                     gagTTTATTAAACGTAATGGCGAATTCACCGTTAACATTGCGCTCATTGACCATGGCAAACCGAttt                                                  <  1:2494625/67‑1 (MQ=255)
                     gagTTTATTAAACGTAATGGCGAATTCACCGTTAACATTGCGCTCATTGACCATGGCAAACCGAttt                                                  <  1:807038/67‑1 (MQ=255)
                     gagTTTATTAAACGTAATGGCGAATTCACCGTTAACATTGCGCTCATTGACCATGGCAAACCGAttt                                                  <  1:2318649/67‑1 (MQ=255)
                     gagTTTATTAAACGTAATGGCGAATTCACCGTTAACATTGCGCTCATTGACCATGGCAAACCGAttt                                                  <  1:2236493/67‑1 (MQ=255)
                     gagTTTATTAAACGTAATGGCGAATTCACCGTTAACATTGCGCTCATTGACCATGGCAAACCGAttt                                                  <  1:3037517/67‑1 (MQ=255)
                     gagTTTATTAAACGTAATGGCGAATTCACCGTTAACATTGCGCTCATTGACCATGGCAAACCGATTTTa                                                >  1:1001424/1‑69 (MQ=255)
                     gagTTTATTAAACGTAATGGCGAATTCACCGTTAACATTGCGCTCATTGACCATGGCAAACCGATTTTa                                                >  1:2411567/1‑69 (MQ=255)
                     gagTTTATTAAACGTAATGGCGAATTCACCGTTAACATTGCGCTCATTGACCATGGCAAACCGATTTTa                                                >  1:2354510/1‑69 (MQ=255)
                     gagTTTATTAAACGTAATGGCGAATTCACCGTTAACATTGCGCTCATTGACCATGGCAAACCGATTTTa                                                >  1:2058138/1‑69 (MQ=255)
                     gagTTTATTAAACGTAATGGCGAATTCACCGTTAACATTGCGCTCATTGACCATGGCAAACCGATTTTa                                                >  1:2072204/1‑69 (MQ=255)
                      agTTTATTAAACGTAATGGCGAATTCACCGTTAACATTGCGCTCATTGACCATGGCAAACCGAttt                                                  <  1:1857124/66‑1 (MQ=255)
                      agTTTATTAAACGTAATGGCGAATTCACCGTTAACATTGCGCTCATTGACCATGGCAAACCGATTTTAg                                               >  1:3083672/1‑69 (MQ=255)
                        tttATTAAACGTAATGGCGAATTCACCGTTAACATTGCGCTCATTGACCATgg                                                             >  1:1530646/1‑53 (MQ=255)
                        tttATTAAACGTAATGGCGAATTCACCGTTAACATTGCGCTCATTGACCATGGCAAACCGATTTTAGGc                                             >  1:3415211/1‑69 (MQ=255)
                        tttATTAAACGTAATGGCGAATTCACCGTTAACATTGCGCTCATTGACCATGGCAAACCGATTTTAGGc                                             >  1:1126549/1‑69 (MQ=255)
                        tttATTAAACGTAATGGCGAATTCACCGTTAACATTGCGCTCATTGACCATGGCAAACCGATTTTAGGc                                             >  1:2976240/1‑69 (MQ=255)
                        tttATTAAACGTAATGGCGAATTCACCGTTAACATTGCGCTCATTGACCATGGCAAACCGATTTTAGGc                                             >  1:1569822/1‑69 (MQ=255)
                         ttattaAACGTAATGGCGAATTCACCGTTAACATTGCGCTCATCGACCACGGTAAACCGATTTTAggtg                                            <  1:1865603/69‑3 (MQ=255)
                         ttattaAACGTAATGGCGAATTCACCGTTAACATTGCGCTCATCGACCACGGTAAACCGATTTTAggtg                                            <  1:1720835/69‑3 (MQ=255)
                         ttattaAACGTAATGGCGAATTCACCGTTAACATTGCGCTCATCGACCACGGTAAACCGATTTTAggtg                                            <  1:1028780/69‑3 (MQ=255)
                         ttattaAACGTAATGGCGAATTCACCGTTAACATTGCGCTCATCGACCACGGTAAACCGATTTTAggtg                                            <  1:2990233/69‑3 (MQ=255)
                         ttattaAACGTAATGGCGAATTCACCGTTAACATTGCGCTCATCGACCACGGTAAACCGATTTTAggtg                                            <  1:586960/69‑3 (MQ=255)
                         ttattaAACGTAATGGCGAATTCACCGTTAACATTGCGCTCATCGACCACGGTAAACCGATTTTAggtg                                            <  1:1941470/69‑3 (MQ=255)
                         ttattaAACGTAATGGCGAATTCACCGTTAACATTGCGCTCATCGACCACGGTAAACCGATTTTAggtg                                            <  1:2023950/69‑3 (MQ=255)
                         ttattaAACGTAATGGCGAATTCACCGTTAACATTGCGCTCATCGACCACGGTAAACCGATTTTAggtg                                            <  1:2848453/69‑3 (MQ=255)
                         ttattaAACGTAATGGCGAATTCACCGTTAACATTGCGCTCATCGACCACGGTAAACCGATTTTAggtg                                            <  1:2863015/69‑3 (MQ=255)
                         ttattaAACGTAATGGCGAATTCACCGTTAACATTGCGCTCATCGACCACGGTAAACCGATTTTAggtg                                            <  1:2866706/69‑3 (MQ=255)
                              aaaCGTAATGGCGAATTCACCGTTAACATTGCGCTCATTGACCATGGCAAACCGATTTTAGGCgtggtg                                       <  1:2470556/69‑1 (MQ=255)
                              aaaCGTAATGGCGAATTCACCGTTAACATTGCGCTCATTGACCATGGCAAACCGATTTTAGGCgtggtg                                       <  1:3324349/69‑1 (MQ=255)
                              aaaCGTAATGGCGAATTCACCGTTAACATTGCGCTCATTGACCATGGCAAACCGATTTTAGGCgtggtg                                       <  1:690999/69‑1 (MQ=255)
                              aaaCGTAATGGCGAATTCACCGTTAACATTGCGCTCATTGACCATGGCAAACCGATTTTAGGCgtggtg                                       <  1:1138219/69‑1 (MQ=255)
                              aaaCGTAATGGCGAATTCACCGTTAACATTGCGCTCATTGACCATGGCAAACCGATTTTAGGCgtggtg                                       <  1:1365854/69‑1 (MQ=255)
                              aaaCGTAATGGCGAATTCACCGTTAACATTGCGCTCATTGACCATGGCAAACCGATTTTAGGCgtggtg                                       <  1:1395509/69‑1 (MQ=255)
                              aaaCGTAATGGCGAATTCACCGTTAACATTGCGCTCATTGACCATGGCAAACCGATTTTAGGCgtggtg                                       <  1:28757/69‑1 (MQ=255)
                              aaaCGTAATGGCGAATTCACCGTTAACATTGCGCTCATTGACCATGGCAAACCGATTTTAGGCgtggtg                                       <  1:2843956/69‑1 (MQ=255)
                              aaaCGTAATGGCGAATTCACCGTTAACATTGCGCTCATTGACCATGGCAAACCGATTTTAGGCgtggtg                                       <  1:1568703/69‑1 (MQ=255)
                              aaaCGTAATGGCGAATTCACCGTTAACATTGCGCTCATTGACCATGGCAAACCGATTTTAGGCgtggtg                                       <  1:260288/69‑1 (MQ=255)
                              aaaCGTAATGGCGAATTCACCGTTAACATTGCGCTCATTGACCATGGCAAACCGATTTTAGGCgtggtg                                       <  1:1686504/69‑1 (MQ=255)
                               aaCGTAATGGCGAATTCACCGTTAACATTGCGCTCATTGACCATGGCAAACCGATTTTAGGCgtggtg                                       <  1:1892181/68‑1 (MQ=255)
                                            aTTCACCGTTAACATTGCGCTCATCGACCACGGTAAACCGATTTTAggtg                                            <  1:2783027/50‑3 (MQ=255)
                                             ttCACCGTTAACATTGCGCTCATTGACCATGGCAAACCGATTTTAGGCgtggtg                                       <  1:139981/54‑1 (MQ=255)
                                             ttCACCGTTAACATTGCGCTCATTGACCATGGCAAACCGATTTTAGGCgtggtg                                       <  1:3430454/54‑1 (MQ=255)
                                             ttCACCGTTAACATTGCGCTCATTGACCATGGCAAACCGATTTTAGGCgtggtg                                       <  1:645077/54‑1 (MQ=255)
                                             ttCACCGTTAACATTGCGCTCATTGACCATGGCAAACCGATTTTAGGCgtggtg                                       <  1:3308970/54‑1 (MQ=255)
                                             ttCACCGTTAACATTGCGCTCATTGACCATGGCAAACCGATTTTAGGCGTGGTGTATGCGCCGGTAATg                        <  1:94448/69‑1 (MQ=255)
                                             ttCACCGTTAACATTGCGCTCATTGACCATGGCAAACCGATTTTAGGCGTGGTGTATGCGCCGGTAATg                        <  1:453340/69‑1 (MQ=255)
                                             ttCACCGTTAACATTGCGCTCATTGACCATGGCAAACCGATTTTAGGCGTGGTGTATGCGCCGGTAATg                        >  1:3170376/1‑69 (MQ=255)
                                             ttCACCGTTAACATTGCGCTCATTGACCATGGCAAACCGATTTTAGGCGTGGTGTATGCGCCGGTAATg                        <  1:3121959/69‑1 (MQ=255)
                                             ttCACCGTTAACATTGCGCTCATTGACCATGGCAAACCGATTTTAGGCGTGGTGTATGCGCCGGTAATg                        >  1:2581027/1‑69 (MQ=255)
                                             ttCACCGTTAACATTGCGCTCATTGACCATGGCAAACCGATTTTAGGCGTGGTGTATGCGCCGGTAATg                        >  1:243171/1‑69 (MQ=255)
                                             ttCACCGTTAACATTGCGCTCATTGACCATGGCAAACCGATTTTAGGCGTGGTGTATGCGCCGGTAATg                        <  1:1398781/69‑1 (MQ=255)
                                             ttCACCGTTAACATTGCGCTCATTGACCATGGCAAACCGATTTTAGGCGTGGTGTATGCGCCGGTAATg                        <  1:2409926/69‑1 (MQ=255)
                                                   gTTAACATTGCGCTCATTGACCATGGCAAACCGATTTTAGGCgtggtg                                       >  1:1871703/1‑48 (MQ=255)
                                                     tAACATTGCGCTCATT‑ACCATGGCAAACCGATTTTAGGCGTGGTGTATGCGCCGGTAATGAACGTAATg               <  1:890246/69‑1 (MQ=255)
                                                      aaCATTGCGCTGATTGACCATGGCAAACCGATTTTAGGCgtggtg                                       <  1:1425385/45‑1 (MQ=255)
                                                      aaCATTGCGCTCATTGACCATGGCAAACCGATTTTAGGCGTGGTGTATGCGCCGGTAATGAACGTAATg               <  1:1005435/69‑1 (MQ=255)
                                                      aaCATTGCGCTCATTGACCATGGCAAACCGATTTTAGGCGTGGTGTATGCGCCGGTAATGAACGTAATg               <  1:3226110/69‑1 (MQ=255)
                                                      aaCATTGCGCTCATTGACCATGGCAAACCGATTTTAGGCGTGGTGTATGCGCCGGTAATGAACGTAATg               <  1:1185182/69‑1 (MQ=255)
                                                      aaCATTGCGCTCATTGACCATGGCAAACCGATTTTAGGCGTGGTGTATGCGCCGGTAATGAACGTAATg               <  1:709314/69‑1 (MQ=255)
                                                      aaCATTGCGCTCATTGACCATGGCAAACCGATTTTAGGCGTGGTGTATGCGCCGGTAATGAACGTAATg               >  1:1785124/1‑69 (MQ=255)
                                                      aaCATTGCGCTCATTGACCATGGCAAACCGATTTTAGGCGTGGTGTATGCGCCGGTAATGAACGTAATg               <  1:2027716/69‑1 (MQ=255)
                                                      aaCATTGCGCTCATTGACCATGGCAAACCGATTTTAGGCGTGGTGTATGCGCCGGTAATGAACGTAATg               <  1:2227585/69‑1 (MQ=255)
                                                      aaCATTGCGCTCATTGACCATGGCAAACCGATTTTAGGCGTGGTGTATGCGCCGGTAATGAACGTAATg               <  1:2252240/69‑1 (MQ=255)
                                                      aaCATTGCGCTCATTGACCATGGCAAACCGATTTTAGGCGTGGTGTATGCGCCGGTAATGAACGTAATg               <  1:601808/69‑1 (MQ=255)
                                                      aaCATTGCGCTCATTGACCATGGCAAACCGATTTTAGGCGTGGTGTATGCGCCGGTAATGAACGTAATg               <  1:585239/69‑1 (MQ=255)
                                                      aaCATTGCGCTCATTGACCATGGCAAACCGATTTTAGGCGTGGTGTATGCGCCGGTAATGAACGTAATg               >  1:560566/1‑69 (MQ=255)
                                                      aaCATTGCGCTCATTGACCATGGCAAACCGATTTTAGGCGTGGTGTATGCGCCGGTAATGAACGTAATg               <  1:2694548/69‑1 (MQ=255)
                                                      aaCATTGCGCTCATTGACCATGGCAAACCGATTTTAGGCGTGGTGTATGCGCCGGTAATGAACGTAATg               >  1:2734314/1‑69 (MQ=255)
                                                          ttGCGCTCATTGACCATGGCAAACCGATTTTAGGCgtggtg                                       <  1:486824/41‑1 (MQ=255)
                                                                    tGACCATGGCAAACCGATTTTAGGCGTGGTGTATGCGCCGGTAATGAACGTAATGTACAGCGCGGCAg  <  1:828080/68‑1 (MQ=255)
                                                                    |                                                                   
GACCCGCTGGATGGTACTAAAGAGTTTATTAAACGTAATGGCGAATTCACCGTTAACATTGCGCTCATTGACCATGGCAAACCGATTTTAGGCGTGGTGTATGCGCCGGTAATGAACGTAATGTACAGCGCGGCAG  >  minE/2885043‑2885178

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