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 1,511,807 G→A 21.5% E359K (GAG→AAG)  pta → phosphate acetyltransferase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,511,8070GA21.5% 201.9 / 50.5 93E359K (GAG→AAG) ptaphosphate acetyltransferase
Reads supporting (aligned to +/- strand):  ref base G (24/49);  new base A (16/4);  total (40/53)
Fisher's exact test for biased strand distribution p-value = 2.41e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.94e-01

Only 100 of 106 total aligned reads displayed.

CACCTGGCAGACCTCTCTGAGCCTGCAGAGCTTCAACCTGGAAGTTCCGGTTGACGATCACGAACGTATCGAGAAAGTTCAGGAATACGTTGCTAACTACATCAACGCTGACTGGATCGAATCTCTGACTGCCACTTCT  >  minE/1511737‑1511875
                                                                      |                                                                    
caccTGGCAGACCTCTCTGAGCCTGCAGAGCTTCAACCTGGAAGTTCCGGTTGGCGATCACGAACGTATCg                                                                      <  1:2234907/71‑1 (MQ=255)
caccTGGCAGACCTCTCTGAGCCTGCAGAGCTTCAACCTGGAAGTTCCGGTTGACGATCACGAACGTATCg                                                                      <  1:2015572/71‑1 (MQ=255)
            ctctctGAGCCTGCAGAGCTTCAACCTGGAAGTTCCGGTTGACGATCACGAACGTATCGAGAAAGTTCAgg                                                          <  1:2609009/71‑1 (MQ=255)
            ctctctGAGCCTGCAGAGCTTCAACCTGGAAGTTCCGGTTGACGATCACGAACGTATCAAGaaa                                                                 >  1:37585/1‑64 (MQ=255)
            ctctctGAGCCTGCAGAGCTTCAACCTGGAAGTTCCGGTTGACGATCACGAACGTATCAAGAAAGTTCAgg                                                          <  1:2068363/71‑1 (MQ=255)
            ctctctGAGCCTGCAGAGCTTCAACCTGGAAGTTCCGGTTGACGATCACGAACGTATCAAGAAAGTTCAgg                                                          <  1:3346144/71‑1 (MQ=255)
              ctctGAGCCTGCAGAGCTTCAACCTGGAAGTTCCGGTTGACGATCACGAACGTATCAAGAAAGTTCAGGaa                                                        >  1:3384474/1‑71 (MQ=255)
               tctGAGCCTGCAGAGCTTCAACCTGGAAGTTCCGGTTGACGATCACGAACGTATCGAGAAAGTTCAGGaa                                                        >  1:3891313/1‑70 (MQ=255)
               tctGAGCCTGCAGAGCTTCAACCTGGAAGTTCCGGTTGACGATCACGAACGTATCGAGAAAGTTCAGGaa                                                        >  1:3789430/1‑70 (MQ=255)
               tctGAGCCTGCAGAGCTTCAACCTGGAAGTTCCGGTTGACGATCACGAACGTATCGAGAAAGTTCAGGaa                                                        >  1:2537736/1‑70 (MQ=255)
               tctGAGCCTGCAGAGCTTCAACCTGGAAGTTCCGGTTGACGATCACGAACGTATCGAGAAAGTTCAGGaa                                                        >  1:2888460/1‑70 (MQ=255)
               tctGAGCCTGCAGAGCTTCAACCTGGAAGTTCCGGTTGACGATCACGAACGTATCAAGAAAGTTCAGGaa                                                        >  1:3059493/1‑70 (MQ=255)
               tctGAGCCTGCAGAGCTTCAACCTGGAAGTTCCGGTTGACGATCACGAACGTATCAAGAAAGTTCAGGaa                                                        >  1:591021/1‑70 (MQ=255)
                   aGCCTGCAGAGCTTCAACCTGGAAGTTCCGGTTGACGATCACGAACGTATCAAGAAAGTTCAGGAATACGt                                                   <  1:2977067/71‑1 (MQ=255)
                   aGCCTGCAGAGCTTCAACCTGGAAGTTCCGGTTGACGATCACGAACGTATCAAGAAAGTTCAGGAATACGt                                                   <  1:4110546/71‑1 (MQ=255)
                      cTGCAGAGCTTCAACCTGGAAGTTCCGGTTGACGATCACGAACGTATCGAGAAAGTTCAGGAATACGTTGc                                                <  1:3859650/71‑1 (MQ=255)
                      cTGCAGAGCTTCAACCTGGAAGTTCCGGTTGACGATCACGAACGTATCGAGAAAGTTCAGGAATACGTTGc                                                <  1:959949/71‑1 (MQ=255)
                       tGCAGAGCTTCAACCTGGAAGTTCCGGTTGACGATCACGAACGTATCGAGAAAGTTCAgg                                                          <  1:3895385/60‑1 (MQ=255)
                       tGCAGAGCTTCAACCTGGAAGTTCCGGTTGACGATCACGAACGTATCGAGAAAGTTCAgg                                                          <  1:3823971/60‑1 (MQ=255)
                       tGCAGAGCTTCAACCTGGAAGTTCCGGTTGACGATCACGAACGTATCGAGAAAGTTCAgg                                                          <  1:676648/60‑1 (MQ=255)
                         cAGAGCTTCAACCTGGAAGTTCCGGTTGACGATCACGAACGTATCGAGAAAGTTCAGGAATACGTTGCTaa                                             >  1:3480927/1‑71 (MQ=255)
                         cAGAGCTTCAACCTGGAAGTTCCGGTTGACGATCACGAACGTATCGAGAAAGTTCAGGAATACGTTGCTaa                                             >  1:602488/1‑71 (MQ=255)
                          agagCTTCAACCTGGAAGTTCCGGTTGACGATCACGAACGTATCGAGAAAGTTCAGGAATACGTTGCTAAc                                            <  1:3658272/71‑1 (MQ=255)
                           gagCTTCAACCTGGAAGTTCCGGTTGACGATCACGAACGTATCGAGTAAGTTCAgg                                                          <  1:500518/56‑1 (MQ=255)
                           gagCTTCAACCTGGAAGTTCCGGTTGACGATCACGAACGTATCAAGAAAGTTCAGGAATACGTTGCTAAc                                            >  1:3314854/1‑70 (MQ=255)
                              cTTCCACCTGGAAGTTCCGGTTGACGATCACGAACGTATCGAGAAAGTTCAGGAAt                                                       <  1:392195/56‑1 (MQ=255)
                              cTTCAACCTGGAAGTTCCGGTTGACGATCACGAACGTATCGAGAAAGTTCAGGAAt                                                       <  1:3659059/56‑1 (MQ=255)
                              cTTCAACCTGGAAGTTCCGGTTGACGATCACGAACGTATCGAGAAAGTTCAGGAAt                                                       <  1:2816393/56‑1 (MQ=255)
                              cTTCAACCTGGAAGTTCCGGTTGACGATCACGAACGTATCGAGAAAGTTCAGGAAt                                                       <  1:870134/56‑1 (MQ=255)
                              cTTCAACCTGGAAGTTCCGGTTGACGATCACGAACGTATCGAGAAAGTTCAGGAAt                                                       <  1:1229601/56‑1 (MQ=255)
                              cTTCAACCTGGAAGTTCCGGTTGACGATCACGAACGTATCGAGAAAGTTCAGGAAt                                                       <  1:3684138/56‑1 (MQ=255)
                              cTTCAACCTGGAAGTTCCGGTTGACGATCACGAACGTATCGAGAAAGTTCAGGAAt                                                       <  1:1363703/56‑1 (MQ=255)
                              cTTCAACCTGGAAGTTCCGGTTGACGATCACGAACGTATCGAGAAAGTTCAGGAATa                                                      <  1:3194744/57‑1 (MQ=255)
                              cTTCAACCTGGAAGTTCCGGTTGACGATCACGAACGTATCGAGAAAGTTCAGGAATa                                                      <  1:4050619/57‑1 (MQ=255)
                              cTTCAACCTGGAAGTTCCGGTTGACGATCACGAACGTATCGAGAAAGTTCAGGAATACGTTGCt                                               <  1:167087/64‑1 (MQ=255)
                              cTTCAACCTGGAAGTTCCGGTTGACGATCACGAACGTATCGAGAAAGTTCAGGAATACGTTGCt                                               <  1:65227/64‑1 (MQ=255)
                                  aaCCTGGAAGTTCCGGTTGACGATCACGAACGTATCAAGAAAGTTCAGGAATACGt                                                   >  1:1392410/1‑56 (MQ=255)
                                  aaCCTGGAAGTTCCGGTTGACGATCACGAACGTATCAAGAAAGTTCAGGAATACGt                                                   >  1:2232129/1‑56 (MQ=255)
                                  aaCCTGGAAGTTCCGGTTGACGATCACGAACGTATAAAGAAAGTTCAGGAATACg                                                    >  1:905283/1‑55 (MQ=39)
                                      tGGAAGTTCCGGTTGACGATCACGAACGTATCGAGAAAGTTCAGGAATAc                                                     <  1:875498/50‑1 (MQ=255)
                                      tGGAAGTTCCGGTTGACGATCACGAACGTATCGAGAAAGTTCAGGAATAc                                                     <  1:3002900/50‑1 (MQ=255)
                                        gAAGTTCCGGTTGACGATCACGAACGTATCGAGAAAGTTCAGGaa                                                        >  1:183914/1‑45 (MQ=255)
                                        gAAGTTCCGGTTGACGATCACGAACGTATCGAGAAAGTTCAGGAATa                                                      <  1:3478315/47‑1 (MQ=255)
                                        gAAGTTCCGGTTGACGATCACGAACGTATCGAGAAAGTTCAGGAATa                                                      <  1:596310/47‑1 (MQ=255)
                                        gAAGTTCCGGTTGACGATCACGAACGTATCGAGAAAGTTCAGGAATa                                                      <  1:1731652/47‑1 (MQ=255)
                                        gAAGTTCCGGTTGACGATCACGAACGTATCGAGAAAGTTCAGGAATa                                                      <  1:1040977/47‑1 (MQ=255)
                                        gAAGTTCCGGTTGACGATCACGAACGTATCGAGAAAGTTCAGGAATACGt                                                   >  1:3516006/1‑50 (MQ=255)
                                        gAAGTTCCGGTTGACGATCACGAACGTATCGAGAAAGTTCAGGAATACGt                                                   >  1:3109803/1‑50 (MQ=255)
                                        gAAGTTCCGGTTGACGATCACGAACGTATCGAGAAAGTTCAGGAATACGt                                                   >  1:2345660/1‑50 (MQ=255)
                                        gAAGTTCCGGTTGACGATCACGAACGTATCGAGAAAGTTCAGGAATACGt                                                   >  1:1105590/1‑50 (MQ=255)
                                        caaGTTCCGGTTGACGATCACGAACGTATCGAGAAAGTTCAGGAATa                                                      <  1:2693249/46‑1 (MQ=255)
                                           gTTCCGGTTGACGATCACGAACGTATCGAGAAAGTTCAGGAATACGTTGCt                                               <  1:383253/51‑1 (MQ=255)
                                           gTTCCGGTTGACGATCACGAACGTATCGAGAAAGTTCAGGAATACGTTGCt                                               <  1:1048944/51‑1 (MQ=255)
                                           gTTCCGGTTGACGATCACGAACGTATCGAGAAAGTTCAGGAATACGTTGCt                                               <  1:2329375/51‑1 (MQ=255)
                                           gTTCCGGTTGACGATCACGAACGTATCGAGAAAGTTCAGGAATACGTTGCt                                               <  1:879086/51‑1 (MQ=255)
                                           gTTCCGGTTGACGATCACGAACGTATCGAGAAAGTTCAGGAATACGTTGCt                                               <  1:1409194/51‑1 (MQ=255)
                                           gTTCCGGTTGACGATCACGAACGTATCGAGAAAGTTCAGGAATACGTTGCt                                               <  1:792634/51‑1 (MQ=255)
                                           gTTCCGGTTGACGATCACGAACGTATCGAGAAAGTTCAGGAATACGTTGCt                                               <  1:2549113/51‑1 (MQ=255)
                                           gTTCCGGTTGACGATCACGAACGTATCGAGAAAGTTCAGGAATACGTTGCt                                               <  1:3392248/51‑1 (MQ=255)
                                           gTTCCGGTTGACGATCACGAACGTATCGAGAAAGTTCAGGAATACGTTGCt                                               <  1:1403522/51‑1 (MQ=255)
                                             tCCGGTTGACGATCACGAACGTATCGAGAAAGTTCAGGAATACGTTGCTAACTACATCAACGCTGACTGGa                         >  1:1240672/1‑71 (MQ=255)
                                             tCCGGTTGACGATCACGAACGTATCGAGAAAGTTCAGGAATACGTTGCTAACTACATCAACGCTGACTGGa                         >  1:1588452/1‑71 (MQ=255)
                                             tCCGGTTGACGATCACGAACGTATCAAGAAAGTTCAGGAATACGTTGCTAACTACATCAACGCTGACTg                           >  1:2743706/1‑69 (MQ=255)
                                             tCCGGTTGACGATCACGAACGTATCAAGAAAGTTCAGGAATACGTTGCTAACTACATCAACGCTGACTg                           >  1:3294466/1‑69 (MQ=255)
                                             tCCGGTTGACGATCACGAACGTATCAAGAAAGTTCAGGAATACGTTGCTAACTACATCAACGCTGACTg                           >  1:4098962/1‑69 (MQ=255)
                                             tCCGGTTGACGATCACGAACGTATCAAGAAAGTTCAGGAATACGTTGCTAACTACATCAACGCTGACTg                           >  1:102331/1‑69 (MQ=255)
                                             tCCGGTTGACGATCACGAACGTATCAAGAAAGTTCAGGAATACGTTGCTAACTACATCAACGCTGACTg                           >  1:1873543/1‑69 (MQ=255)
                                             tCCGGTTGACGATCACGAACGTATCAAGAAAGTTCAGGAATACGTTGCTAACTACATCAACGCTGACTg                           >  1:2001476/1‑69 (MQ=255)
                                             tCCGGTTGACGATCACGAACGTATCAAGAAAGTTCAGGAATACGTTGCTAACTACATCAACGCTGACTg                           >  1:2176732/1‑69 (MQ=255)
                                             tCCGGTTGACGATCACGAACGTATCAAGAAAGTTCAGGAATACGTTGCTAACTACATCAACGCTGACTg                           >  1:2924531/1‑69 (MQ=255)
                                                ggTTGACGATCACGAACGTATCGAGAAAGTTCAGGAATACGTTGCTAACTACATCAACGCTGACTGGATCg                      <  1:2548484/71‑1 (MQ=255)
                                                    gACGATCACGAACGTATCGAGAAAGTTCAGGAATACGTTGCTAACTACATCAACGCTGTCTGGATCGAAtc                  >  1:1440846/1‑71 (MQ=255)
                                                    gACGATCACGAACGTATCGAGAAAGTTCAGGAATACGTTGCTAACTACATCAACGCTGACTGGATCGAAtc                  >  1:1362414/1‑71 (MQ=255)
                                                    gACGATCACGAACGTATCGAGAAAGTTCAGGAATACGTTGCTAACTACATCAACGCTGACTGGATCGAAtc                  >  1:1028840/1‑71 (MQ=255)
                                                    gACGATCACGAACGTATCGAGAAAGTTCAGGAATACGTTGCTAACTACATCAACGCTGACTGGATCGAAtc                  >  1:884829/1‑71 (MQ=255)
                                                    gACGATCACGAACGTATCGAGAAAGTTCAGGAATACGTTGCTAACTACATCAACGCTGACTGGATCGAAtc                  >  1:2285472/1‑71 (MQ=255)
                                                       gATCACGAACGTATCGAGAAAGTTCAGGAATACGTTGCTAACTACATCAACGCTGACTGGATCGAATctct               <  1:699196/71‑1 (MQ=255)
                                                          cACGAACGTATCGAGAAAGTTCAGGAATACGTTGCTAACTACATCAACGCTGACTGGATCGAATCTCTGAc            >  1:3445088/1‑71 (MQ=255)
                                                                  tATCGAGAAAGTTCAGGAATACGTTGCTAACTACATCAACGCTGACTGGATCGAATCTCTGACTGCCACtt    <  1:110825/71‑1 (MQ=255)
                                                                  tATCGAGAAAGTTCAGGAATACGTTGCTAACTACATCAACGCTGACTGGATCGAATCTCTGACTGCCACtt    <  1:1861959/71‑1 (MQ=255)
                                                                    tCGAGAAAGTTCAGGAATACGTTGCTAACTACATCATCGCt                                <  1:639765/41‑1 (MQ=255)
                                                                    tCGAGAAAGTTCAGGAATACGTTGCTAACTACATCAACGCt                                <  1:3149513/41‑1 (MQ=255)
                                                                    tCGAGAAAGTTCAGGAATACGTTGCTAACTACATCAACGCt                                <  1:3348148/41‑1 (MQ=255)
                                                                    tCGAGAAAGTTCAGGAATACGTTGCTAACTACATCAACGCt                                <  1:3432330/41‑1 (MQ=255)
                                                                    tCGAGAAAGTTCAGGAATACGTTGCTAACTACATCAACGCt                                <  1:2251357/41‑1 (MQ=255)
                                                                    tCGAGAAAGTTCAGGAATACGTTGCTAACTACATCAACGCTGACTGGATCGAATCTCTGACTGCCACTTCt  <  1:886654/71‑1 (MQ=255)
                                                                    tCGAGAAAGTTCAGGAATACGTTGCTAACTACATCAACGCTGACTGGATCGAATCTCTGACTGCCACTTCt  <  1:27795/71‑1 (MQ=255)
                                                                    tCGAGAAAGTTCAGGAATACGTTGCTAACTACATCAACGCTGACTGGATCGAATCTCTGACTGCCACTTCt  <  1:169672/71‑1 (MQ=255)
                                                                     cGAGAAAGTTCAGGAATACGTTGCTAACTACATCAACGCTGACTGGATCGAATCTCTCACTGCCACTTCt  <  1:3699083/70‑1 (MQ=255)
                                                                      gagaAAGTTCAGGAATACGTTGCTAACTACATCAACGCTGa                              >  1:2496145/1‑41 (MQ=255)
                                                                      gagaAAGTTCAGGAATACGTTGCTAACTACATCAACGCTGa                              >  1:2448623/1‑41 (MQ=255)
                                                                      gagaAAGTTCAGGAATACGTTGCTAACTACATCAACGCTGACTGGATCGaa                    >  1:3312895/1‑51 (MQ=255)
                                                                      gagaAAGTTCAGGAATACGTTGCTAACTACATCAACGCTGACTGGATCGaa                    >  1:3786243/1‑51 (MQ=255)
                                                                      gagaAAGTTCAGGAATACGTTGCTAACTACATCAACGCTGACTGGATCGaa                    >  1:675910/1‑51 (MQ=255)
                                                                      gagaAAGTTCAGGAATACGTTGCTAACTACATCAACGCTGACTGGATCGaa                    >  1:2021280/1‑51 (MQ=255)
                                                                      gagaAAGTTCAGGAATACGTTGCTAACTACATCAACGCTGACTGGATCGAAtct                 >  1:3373349/1‑54 (MQ=255)
                                                                      gagaAAGTTCAGGAATACGTTGCTAACTACATCAACGCTGACTGGATCGAATCTCTGACTGCCACTTc   >  1:3043656/1‑68 (MQ=255)
                                                                      gagaAAGTTCAGGAATACGTTGCTAACTACATCAACGCTGACTGGATCGAATCTCTGACTGCCACTTCt  >  1:1231562/1‑69 (MQ=255)
                                                                      gagaAAGTTCAGGAATACGTTGCTAACTACATCAACGCTGACTGGATCGAATCTCTGACTGCCACTTCt  >  1:3397380/1‑69 (MQ=255)
                                                                      gagaAAGTTCAGGAATACGTTGCTAACTACATCAACGCTGACTGGATCGAATCTCTGACTGCCACTTCt  >  1:1432276/1‑69 (MQ=255)
                                                                      |                                                                    
CACCTGGCAGACCTCTCTGAGCCTGCAGAGCTTCAACCTGGAAGTTCCGGTTGACGATCACGAACGTATCGAGAAAGTTCAGGAATACGTTGCTAACTACATCAACGCTGACTGGATCGAATCTCTGACTGCCACTTCT  >  minE/1511737‑1511875

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