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
A6 F1 I0 R1 2892 75.3 5698161 66.1% 3766484 59.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,569,866 A→G 30.9% T46A (ACG→GCG) ‡ yibI → predicted inner membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,569,8660AG30.9% 166.6 / 106.5 136T46A (ACG→GCG) ‡yibIpredicted inner membrane protein
Reads supporting (aligned to +/- strand):  ref base A (41/53);  new base G (22/20);  total (63/73)
Fisher's exact test for biased strand distribution p-value = 3.59e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.76e-01

Only 100 of 141 total aligned reads displayed.

ATCGCGATACATGACATCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCTGTGGATCTGGGCGACGCTC  >  minE/2569797‑2569934
                                                                     |                                                                    
atcGCGATACATGACATCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATa                                                                      >  1:852705/1‑70 (MQ=255)
atcGCGATACATGACATCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATa                                                                      >  1:1243472/1‑70 (MQ=255)
atcGCGATACATGACATCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATa                                                                      <  1:1477907/70‑1 (MQ=255)
       tACATGACATCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATAcggc                                                                  <  1:2005412/67‑1 (MQ=255)
       tACATGACATCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATAcggc                                                                  <  1:1745259/67‑1 (MQ=255)
       tACATGACATCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATAcggc                                                                  <  1:3118730/67‑1 (MQ=255)
         cATGACATCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCt                                                             <  1:2381209/70‑1 (MQ=255)
         cATGACATCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTg                                                            >  1:4990284/1‑71 (MQ=255)
                tCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGc                                                     <  1:4346774/71‑1 (MQ=255)
                  ccTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCt                                                   >  1:2166381/1‑71 (MQ=255)
                    ttATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGt                                                 >  1:2197050/1‑71 (MQ=255)
                     tATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTgg                                                           <  1:3690337/60‑1 (MQ=255)
                     tATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGtt                                                >  1:3801171/1‑71 (MQ=255)
                     tATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGtt                                                >  1:3100864/1‑71 (MQ=255)
                      accTGATTGCCAAAAAACGTAATCATCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCtttt                                                >  1:4720228/3‑70 (MQ=255)
                      accTGATTGCCAAAAAACGTAATCATCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCtttt                                                >  1:4671916/3‑70 (MQ=255)
                      accTGATTGCCAAAAAACGTAATCATCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCtttt                                                >  1:3829765/3‑70 (MQ=255)
                      aTCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGtt                                                >  1:5463544/1‑70 (MQ=255)
                      aTCTGATTGCCAAAAAGCGCAACCATCCCAATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGtt                                                >  1:1190558/1‑70 (MQ=255)
                       tCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATAcgg                                                                   >  1:802442/1‑50 (MQ=255)
                       ccTGATTGCCAAAAAACGTAATCATCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCtttt                                                <  1:3537745/68‑1 (MQ=255)
                        cTGATTGCCAAAAAACGTAATCATCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCttt                                                 <  1:2727207/67‑3 (MQ=255)
                        cTGATTGCCAAAAAACGTAATCATCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTtttt                                               <  1:4888679/69‑1 (MQ=255)
                        cTGATTGCCAAAAAACGTAATCATCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTAc                                             <  1:1573822/71‑1 (MQ=255)
                         tGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTAct                                            >  1:4354769/1‑71 (MQ=255)
                          gATTGCCAAAAAACGTAATCATCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTAcgt                                           >  1:5291234/1‑69 (MQ=255)
                          gATTGCCAAAAAACGTAATCATCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTAcgt                                           >  1:172019/1‑69 (MQ=255)
                           aTTGCCAAAAAGCGCAACCATCCTCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTAc                                             <  1:5367204/68‑1 (MQ=255)
                           aTTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTActct                                          >  1:2202953/1‑71 (MQ=255)
                            ttGCCGAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTActct                                          >  1:3191869/1‑70 (MQ=255)
                            ttGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTg                                         <  1:4366441/71‑1 (MQ=255)
                            ttGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTg                                         >  1:1663345/1‑71 (MQ=255)
                             tGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTg                                         >  1:992449/1‑70 (MQ=255)
                              gCCAAAAAACGTAATCATCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTa                                              >  1:3065113/1‑64 (MQ=255)
                                 aaaaaaCGTAATCATCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTACGTTACATGt                                    >  1:2334898/1‑71 (MQ=255)
                                 aaaaaGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGt                                    >  1:3214145/1‑71 (MQ=255)
                                  aaaaGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTa                                              >  1:933933/1‑60 (MQ=255)
                                  aaaaGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTa                                              >  1:5133009/1‑60 (MQ=255)
                                  aaaaGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGt                                    >  1:722329/1‑70 (MQ=255)
                                  aaaaGCGCAACCATCCCCAAGCCGACGCTATTCATAcggcgg                                                                >  1:2823040/1‑42 (MQ=255)
                                  aaaaACGTAATCATCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTACGTTACATGt                                    >  1:4942626/1‑70 (MQ=255)
                                    aaGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTgg                                                           >  1:2292439/1‑45 (MQ=255)
                                    aaGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTgg                                                           >  1:780185/1‑45 (MQ=255)
                                     aGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATc                                <  1:5297502/71‑1 (MQ=255)
                                     aGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATc                                <  1:5631368/71‑1 (MQ=255)
                                     aGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATc                                <  1:22948/71‑1 (MQ=255)
                                      gcgcAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCt                               <  1:79918/71‑1 (MQ=255)
                                       cgcAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTg                              >  1:4147305/1‑71 (MQ=255)
                                          aaCCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATc                                <  1:3414335/66‑1 (MQ=255)
                                           atcATCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTACGTTACATGTTa                                  >  1:1354295/3‑63 (MQ=255)
                                            tcATCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTACGTTACATGTTa                                  <  1:2660539/61‑1 (MQ=255)
                                            tcATCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTACGTTACATGTTa                                  <  1:1396186/61‑1 (MQ=255)
                                            tcATCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTACGTTACATGTTa                                  <  1:5340909/61‑1 (MQ=255)
                                            tcATCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTACGTTACATGTTAt                                 >  1:3518308/2‑63 (MQ=255)
                                            tcATCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTACGTTACATGTTATCTGGCCGt                         <  1:1009023/70‑1 (MQ=255)
                                            ccATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGt                         <  1:2571623/71‑1 (MQ=255)
                                            ccATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGt                         <  1:4374643/71‑1 (MQ=255)
                                            ccATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGt                         <  1:515595/71‑1 (MQ=255)
                                            ccATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGt                         <  1:660972/71‑1 (MQ=255)
                                             cATCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTACGTTACATGt                                    >  1:2114441/1‑59 (MQ=255)
                                              aTCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTACGTTACATGtt                                   >  1:5651686/1‑59 (MQ=255)
                                              aTCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTACGTTACATGtt                                   >  1:3210049/1‑59 (MQ=255)
                                              aTCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGttt                       <  1:5020467/71‑1 (MQ=255)
                                              aTCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGtt                        >  1:4722256/1‑70 (MQ=255)
                                               tCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTAcgt                                           <  1:1132009/50‑3 (MQ=255)
                                               tCCTCATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTAcgt                                           <  1:2048407/50‑3 (MQ=255)
                                               tCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGtt                                                <  1:2935852/45‑1 (MQ=255)
                                               tCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTc                      <  1:1196356/71‑1 (MQ=255)
                                               tCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTc                      <  1:1489890/71‑1 (MQ=255)
                                               accccATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCt                                                   <  1:3960212/41‑1 (MQ=255)
                                                 ctcATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTACGTTACATGTTATCTGGCCGTTTTtg                    >  1:2797549/3‑71 (MQ=255)
                                                 cccATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCtg                    <  1:2724093/71‑1 (MQ=255)
                                                 cccATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCtg                    <  1:2518199/71‑1 (MQ=255)
                                                 cccATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCt                     >  1:4563581/1‑70 (MQ=255)
                                                 cccATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCt                     <  1:3068120/70‑1 (MQ=255)
                                                 cccATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCt                     <  1:3899699/70‑1 (MQ=255)
                                                 cccATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCt                     <  1:1131859/70‑1 (MQ=255)
                                                  tcATGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTACGTTACATGTTATCTGGCCGttttt                     <  1:3591591/68‑3 (MQ=255)
                                                   cATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCt                     <  1:1049063/68‑1 (MQ=255)
                                                    aTGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTACGTTACATGTTATCTGGCCGTTTTtg                    <  1:5633290/68‑1 (MQ=255)
                                                    aTGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTACGTTACATGTTATCTGGCCGTTTTTGTgg                 <  1:1260818/71‑1 (MQ=255)
                                                     tGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTAct                                            <  1:3876431/43‑1 (MQ=255)
                                                     tGCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTACGTTACATGTTATCTGGCCGTTTTTGTGGa                <  1:1399860/71‑1 (MQ=255)
                                                      gCCGACGCTATTCATACGGCTGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCTGTGGa                <  1:469848/70‑1 (MQ=255)
                                                      gCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTACGTTACATGTTATCTGGCCGttttt                     >  1:1053594/1‑63 (MQ=255)
                                                      gCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTACGTTACATGTTATCTGGCCGTTTTtg                    >  1:1212457/1‑66 (MQ=255)
                                                      gCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTACGTTACATGTTATCTGGCCGTTTTtg                    >  1:5564650/1‑66 (MQ=255)
                                                      gCCGACGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTACGTTACATGTTATCTGGCCGTTTTTGTGGAt               >  1:5610432/1‑71 (MQ=255)
                                                          aCGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGGCGTTTCTGTGGATCTg            <  1:4249926/70‑1 (MQ=255)
                                                           cGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTACGTTACATGTTATCTGGCCGt                         <  1:3773534/56‑1 (MQ=255)
                                                           cGCCATTCATGTTGCTGGTTGGGTGAGTCTTTTTACGTTACATGTTATCTGGCCGTTTTTGTGGATTTggg          <  1:3254356/71‑1 (MQ=255)
                                                               aTTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCa                                       <  1:2225296/38‑1 (MQ=255)
                                                                ttCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGtt                                   <  1:4987888/41‑1 (MQ=255)
                                                                 tCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCTGTgg                 >  1:1897592/1‑58 (MQ=255)
                                                                  cATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCTGTGGATCTGGGCGACg     >  1:4651877/1‑69 (MQ=255)
                                                                  cATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCTGTGGATCTGGGCGACGc    >  1:876759/1‑70 (MQ=255)
                                                                   aTACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGtt                                   <  1:35103/38‑1 (MQ=255)
                                                                   aTACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGtt                                   <  1:4698348/38‑1 (MQ=255)
                                                                   aTACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCTGTGGATCTGGGCGACGctc  <  1:17661/71‑1 (MQ=255)
                                                                     aCGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCTGTGGATCTg            >  1:4947383/1‑59 (MQ=255)
                                                                     |                                                                    
ATCGCGATACATGACATCCCTTATCTGATTGCCAAAAAGCGCAACCATCCCCATGCCGACGCTATTCATACGGCGGGCTGGGTGAGCCTGTTTACTCTGCATGTTATCTGGCCGTTTCTGTGGATCTGGGCGACGCTC  >  minE/2569797‑2569934

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