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 400,786 A→C 46.6% G250G (GGT→GGG)  dacA ← D‑alanyl‑D‑alanine carboxypeptidase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE400,7860AC46.6% ‑5.9 / 120.1 101G250G (GGT→GGG) dacAD‑alanyl‑D‑alanine carboxypeptidase
Reads supporting (aligned to +/- strand):  ref base A (30/24);  new base C (31/16);  total (61/40)
Fisher's exact test for biased strand distribution p-value = 3.14e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.83e-01

Only 100 of 102 total aligned reads displayed.

GTACGTCCGCCCATTACCGCAGAAATCAAGCGCATCTGGCCTTCAGTCGCAGAAGCAACAAGGTTGTAACCTGCTTTGTCAGTGTGTCCGGTTTTGATGCCGTCGACATTCAGGCTGTTATCCCAT  >  minE/400718‑400843
                                                                    |                                                         
gTACGTCCGCCCATTACCGCAGAAATCAAGCGCATCTGGCCTTCAGTCGCAGAAGCAACAAGGTTGTaa                                                           <  1:2440653/69‑1 (MQ=255)
           cATTACCGCAGAAATCAAGCGCATCTGGCCTTCAGTCGCAGAAGCAACAAGGTTGTAACCTGCTTTGTc                                                <  1:926641/69‑1 (MQ=255)
           cATTACCGCAGAAATCAAGCGCATCTGGCCTTCAGTCGCAGAAGCAACAAGGTTGTAACCTGCTTTGTc                                                <  1:2377733/69‑1 (MQ=255)
            aTTACCGCAGAAATCAAGCGCATCTGGCCTTCAGTCGCAGAAGCAACAAGGTTGTAACCTGCTTTGTc                                                <  1:2924463/68‑1 (MQ=255)
              caCCGCAGAGATCAAGCGCATCTGGCCTTCAGTCGCAGAAGCAACAAGGTTGTACCCTGCTTTGTCAgt                                             <  1:2870672/68‑1 (MQ=255)
              caCCGCAGAGATCAAGCGCATCTGGCCTTCAGTCGCAGAAGCAACAAGGTTGTACCCTGCTTTGTCAgt                                             <  1:1781601/68‑1 (MQ=255)
              caCCGCAGAGATCAAGCGCATCTGGCCTTCAGTCGCAGAAGCAACAAGGTTGTACCCTGCTTTGTCAgt                                             <  1:2327276/68‑1 (MQ=255)
              caCCGCAGAGATCAAGCGCATCTGGCCTTCAGTCGCAGAAGCAACAAGGTTGTACCCTGCTTTGTCAgt                                             <  1:2859511/68‑1 (MQ=255)
              caCCGCAGAGATCAAGCGCATCTGGCCTTCAGTCGCAGAAGCAACAAGGTTGTACCCTGCTTTGTCAgt                                             <  1:266366/68‑1 (MQ=255)
              caCCGCAGAGATCAAGCGCATCTGGCCTTCAGTCGCAGAAGCAACAAGGTTGTACCCTGCTTTGTCAgt                                             <  1:3372639/68‑1 (MQ=255)
              caCCGCAGAGATCAAGCGCATCTGGCCTTCAGTCGCAGAAGCAACAAGGTTGTACCCTGCTTTGTCAgt                                             <  1:1458712/68‑1 (MQ=255)
              caCCGCAGAGATCAAGCGCATCTGGCCTTCAGTCGCAGAAGCAACAAGGTTGTACCCTGCTTTGTCAgt                                             <  1:2822557/68‑1 (MQ=255)
              caCCGCAGAGATCAAGCGCATCTGGCCTTCAGTCGCAGAAGCAACAAGGTTGTACCCTGCTTTGTCAgt                                             <  1:1336680/68‑1 (MQ=255)
              caCCGCAGAGATCAAGCGCATCTGGCCTTCAGTCGCAGAAGCAACAAGGTTGTACCCTGCTTTGTCAgt                                             <  1:251038/68‑1 (MQ=255)
              caCCGCAGAGATCAAGCGCATCTGGCCTTCAGTCGCAGAAGCAACAAGGTTGTACCCTGCTTTGTCAgt                                             <  1:2765048/68‑1 (MQ=255)
              caCCGCAGAGATCAAGCGCATCTGGCCTTCAGTCGCAGAAGCAACAAGGTTGTACCCTGCTTTGTCAgt                                             <  1:543609/68‑1 (MQ=255)
              caCCGCAGAGATCAAGCGCATCTGGCCTTCAGTCGCAGAAGCAACAAGGTTGTACCCTGCTTTGTCAgt                                             <  1:1213183/68‑1 (MQ=255)
              caCCGCAGAGATCAAGCGCATCTGGCCTTCAGTCGCAGAAGCAACAAGGTTGTACCCTGCTTTGTCAgt                                             <  1:882000/68‑1 (MQ=255)
              caCCGCAGAGATCAAGCGCATCTGGCCTTCAGTCGCAGAAGCAACAAGGTTGTACCCTGCTTTGTCAgt                                             <  1:2755750/68‑1 (MQ=255)
              caCCGAAGAGATCAAGCGCATCTGGCCTTCAGTCGCAGAAGCAACAAGGTTGTACCCTGCTTTGTCAgt                                             <  1:2839680/68‑1 (MQ=255)
               aCCGCAGAAATCAAGCGCATCTGGCCTTCAGTCGCAGAAGCAACAAGGTTGTAACCTGCTTTGTCAgtg                                            >  1:3349195/1‑69 (MQ=255)
               aCCGCAGAAATCAAGCGCATCTGGCCTTCAGTCGCAGAAGCAACAAGGTTGTAACCTGCTTTGTCAgtg                                            >  1:3193962/1‑69 (MQ=255)
               aCCGCAGAAATCAAGCGCATCTGGCCTTCAGTCGCAGAAGCAACAAGGTTGTAACCTGCTTTGTCAgtg                                            >  1:1866617/1‑69 (MQ=255)
               aCCGCAGAAATCAAGCGCATCTGGCCTTCAGTCGCAGAAGCAACAAGGTTGTAACCTGCTTTGTCAgtg                                            >  1:2236843/1‑69 (MQ=255)
               aCCGCAGAAATCAAGCGCATCTGGCCTTCAGTCGCAGAAGCAACAAGGTTGTAACCTGCTTTGTCAgt                                             >  1:2322563/1‑68 (MQ=255)
               aCCGCAGAAATCAAGCGCATCTGGCCTTCAGACGCAGAAGCAACAAGGTTGTAACCTGCTTAGTCActg                                            >  1:2297574/1‑69 (MQ=255)
                 cGCAGAAATCAAGCGCATCTGGCCTTCAGTCGCAGAAGCAACAAGGTTGTAACCTGCTTTGTCAgtgtg                                          >  1:2748250/1‑69 (MQ=255)
                 cGCAGAAATCAAGCGCATCTGGCCTTCAGTCGCAGAAGCAACAAGGTTGTAACCTGCTTTGTCAgtgtg                                          >  1:1280945/1‑69 (MQ=255)
                 cGCAGAAATCAAGCGCATCTGGCCTTCAGTCGCAGAAGCAACAAGGTTGTAACCTGCTTTGTCAgtgtg                                          >  1:1176219/1‑69 (MQ=255)
                 cGCAGAAATCAAGCGCATCTGGCCTTCAGTCGCAGAAGCAACAAGGTTGTAACCTGCTTTGTCAgtgtg                                          >  1:1007921/1‑69 (MQ=255)
                 cGCAGAAATCAAGCGCATCTGGCCTTCAGTCGCAGAAGCAACAAGGTTGTAACCTGCTTTGTCAgtgt                                           >  1:3041806/1‑68 (MQ=255)
                 cGCAGAAATCAAGCGCATCTAGCCTTCAGTCGCAGAAGCAACAAGGTTGTAACCTGCTTTGTCAgtgtg                                          >  1:1692524/1‑69 (MQ=255)
                    agagATCAAGCGCATCTGGCCTTCAGTCGCAGAAGCAACAAGGTTGTACCCTGCTTTGTCAGTGTGTcc                                       >  1:2304628/1‑69 (MQ=255)
                    agagATCAAGCGCATCTGGCCTTCAGTCGCAGAAGCAACAAGGTTGTACCCTGCTTTGTCAGTGTGTcc                                       >  1:2553276/1‑69 (MQ=255)
                    agagATCAAGCGCATCTGGCCTTCAGTCGCAGAAGCAACAAGGTTGTACCCTGCTTTGTCAGTGTGTcc                                       >  1:2550008/1‑69 (MQ=255)
                    agagATCAAGCGCATCTGGCCTTCAGTCGCAGAAGCAACAAGGTTGTACCCTGCTTTGTCAGTGTGTcc                                       >  1:2407055/1‑69 (MQ=255)
                    agagATCAAGCGCATCTGGCCTTCAGTCGCAGAAGCAACAAGGTTGTACCCTGCTTTGTCAGTGTGTcc                                       >  1:2101021/1‑69 (MQ=255)
                    agagATCAAGCGCATCTGGCCTTCAGTCGCAGAAGCAACAAGGTTGTACCCTGCTTTGTCAGTGTGTcc                                       >  1:2094604/1‑69 (MQ=255)
                    agagATCAAGCGCATCTGGCCTTCAGTCGCAGAAGCAACAAGGTTGTACCCTGCTTTGTCAGTGTGTcc                                       >  1:2932663/1‑69 (MQ=255)
                    agagATCAAGCGCATCTGGCCTTCAGTCGCAGAAGCAACAAGGTTGTACCCTGCTTTGTCAGTGTGTcc                                       >  1:1739470/1‑69 (MQ=255)
                    agagATCAAGCGCATCTGGCCTTCAGTCGCAGAAGCAACAAGGTTGTACCCTGCTTTGTCAGTGTGTcc                                       >  1:3183521/1‑69 (MQ=255)
                    agagATCAAGCGCATCTGGCCTTCAGTCGCAGAAGCAACAAGGTTGTACCCTGCTTTGTCAGTGTGTcc                                       >  1:3342583/1‑69 (MQ=255)
                    agagATCAAGCGCATCTGGCCTTCAGTCGCAGAAGCAACAAGGTTGTACCCTGCTTTGTCAGTGTGTcc                                       >  1:1476572/1‑69 (MQ=255)
                    agagATCAAGCGCATCTGGCCTTCAGTCGCAGAAGCAACAAGGTTGTACCCTGCTTTGTCAGTGTGTcc                                       >  1:3393761/1‑69 (MQ=255)
                    agagATCAAGCGCATCTGGCCTTCAGTCGCAGAAGCAACAAGGTTGTACCCTGCTTTGTCAGTGTGTcc                                       >  1:1312102/1‑69 (MQ=255)
                    agagATCAAGCGCATCTGGCCTTCAGTCGCAGAAGCAACAAGGTTGTACCCTGCTTTGTCAGTGTGTcc                                       >  1:630595/1‑69 (MQ=255)
                    agagATCAAGCGCATCTGGCCTTCAGTCGCAGAAGCAACAAGGTTGTACCCTGCTTTGTCAGTGTGTc                                        >  1:1121268/1‑68 (MQ=255)
                    agagATCAAGCGCATCTGGCCTACAGTCGCATAAGCAACAAGGTTGTACCCTGCTTTGTCAGTGTGTc                                        >  1:2382887/1‑68 (MQ=255)
                          cAAGCGCATCTGGCCTTCAGTCGCATAAGCAACAAGGTTGTAACCTGCTTTGTCAGTGTGTCCGGtttt                                 <  1:1247601/69‑1 (MQ=255)
                          cAAGCGCATCTGGCCTTCAGTCGCAGAAGCAACAAGGTTGTAACCTGCTTTGTCAGTGTGTCCGGtttt                                 <  1:2362890/69‑1 (MQ=255)
                          cAAGCGCATCTGGCCTTCAGTCGCAGAAGCAACAAGGTTGTAACCTGCTTTGTCAGTGTGTCCGGtttt                                 <  1:1681909/69‑1 (MQ=255)
                          cAAGCGCATCTGGCCTTCAGTCGCAGAAGCAACAAGGTTGTAACCTGCTTTGTCAGTGTGTCCGGtttt                                 <  1:2242744/69‑1 (MQ=255)
                                    tGGCCTTCAGTCGCAGAAGCAACAAGGTTGTGACCTGCTTTGTCAGTGTGTCCGGTTTTGATGCCGTc                        >  1:2971251/1‑68 (MQ=255)
                                    tGGCCTTCAGTCGCAGAAGCAACAAGGTTGTAACCTGCTTTGTCAGTGTGTCCGGTTTTGATGCCGTc                        >  1:2397827/1‑68 (MQ=255)
                                    tGGCCTTCAGTCGCAGAAGCAACAAGGTTGTAACCTGCTTTGTCAGTGTGTCCGGTTTTGATGCCGTc                        >  1:1893522/1‑68 (MQ=255)
                                    tGGCCTTCAGTCGCAGAAGCAACAAGGTTGTAACCTGCTTTGTCAGTGTGTCCGGTTTTGATGCCGTc                        >  1:1369983/1‑68 (MQ=255)
                                    tGGCCTTCAGTCGCAGAAGCAACAAGGTTGTAACCTGCTTTGTCAGTGTGTCCGGTTTTGATGCCGTc                        >  1:1819071/1‑68 (MQ=255)
                                               cGCAGAAGCAACAAGGTTGTAACCTGCTTTGTCAGTGTGTCCGGTTTTGATGCCGTCGACATTCAGGCt            >  1:2805012/1‑69 (MQ=255)
                                                gCAGAAGCAACAAGGTTGTAACCTGCTTTGTCAGTGTGTCCGGtttt                                 >  1:302832/1‑47 (MQ=255)
                                                gCAGAAGCAACAAGGTTGTAACCTGCTTTGTCAGTGTGTCCGGtttt                                 >  1:3217788/1‑47 (MQ=255)
                                                gCAGAAGCAACAAGGTTGTAACCTGCTTTGTCAGTGTGTCCGGtttt                                 >  1:1482673/1‑47 (MQ=255)
                                                gCAGAAGCAACAAGGTTGTAACCTGCTTTGTCAGTGTGTCCGGtttt                                 >  1:750601/1‑47 (MQ=255)
                                                gCAGAAGCAACAAGGTTGTAACCTGCTTTGTCAGTGTGTCCGGtttt                                 >  1:2896502/1‑47 (MQ=255)
                                                gCAGAAGCAACAAGGTTGTAACCTGCTTTGTCAGTGTGTCCGGtttt                                 >  1:1198194/1‑47 (MQ=255)
                                                gCAGAAGCAACAAGGTTGTAACCTGCTTTGTCAGTGTGTCCGGtttt                                 >  1:2380831/1‑47 (MQ=255)
                                                gCAGAAGCAACAAGGTTGTAACCTGCTTTGTCAGTGTGTCCGGtttt                                 >  1:2577085/1‑47 (MQ=255)
                                                gCAGAAGCAACAAGGTTGTAACCTGCTTTGTCAGTGTGTCCGGtttt                                 >  1:2762040/1‑47 (MQ=255)
                                                gCAGAAGCAACAAGGTTGTAACCTGCTTTGTCAGTGTGTCCGGtttt                                 >  1:2743353/1‑47 (MQ=255)
                                                gCAGAAGCAACAAGGTTGTAACCTGCTTTGTCAGTGTGTCCAGtttt                                 >  1:643360/1‑47 (MQ=255)
                                                  aGAAGCAACAAGGTTGTACCCTGCTTTGTCAGTGTGTCCGGttt                                  >  1:1953232/1‑44 (MQ=255)
                                                  aGAAGCAACAAGGTTGTACCCTGCTTTGTCAGTGTGTCCGGttt                                  >  1:885478/1‑44 (MQ=255)
                                                  aGAAGCAACAAGGTTGTACCCTGCTTTGTCAGTGTGTCCGGttt                                  >  1:717121/1‑44 (MQ=255)
                                                  aGAAGCAACAAGGTTGTACCCTGCTTTGTCAGTGTGTCCGGttt                                  >  1:2592034/1‑44 (MQ=255)
                                                  aGAAGCAACAAGGTTGTACCCTGCTTTGTCAGTGTGTCCGGttt                                  >  1:14975/1‑44 (MQ=255)
                                                  aGAAGCAACAAGGTTGTACCCTGCTTTGTCAGTGTGTCCGGttt                                  >  1:887311/1‑44 (MQ=255)
                                                  aGAAGCAACAAGGTTGTACCCTGCTTTGTCAGTGTGTCCGGttt                                  >  1:2355601/1‑44 (MQ=255)
                                                  aGAAGCAACAAGGTTGTACCCTGCTTTGTCAGTGTGTCCGGttt                                  >  1:1551787/1‑44 (MQ=255)
                                                  aGAAGCAACAAGGTTGTACCCTGCTTTGTCAGTGTGTCCGGttt                                  >  1:2726165/1‑44 (MQ=255)
                                                  aGAAGCAACAAGGTTGTACCCTGCTTTGTCAGTGTGTCCGGttt                                  >  1:2426939/1‑44 (MQ=255)
                                                  aGAAGCAACAAGGTTGTACCCTGCTTTGTCAGTGTGTCCGGttt                                  >  1:2201977/1‑44 (MQ=255)
                                                  aGAAGCAACAAGGTTGTACCCTGCTTTGTCAGTGTGTCCGGttt                                  >  1:2125582/1‑44 (MQ=255)
                                                  aGAAGCAACAAGGTTGTACCCTGCTTTGTCAGTGTGTCCGGttt                                  >  1:1671569/1‑44 (MQ=255)
                                                  aGAAGCAACAAGGTTGTACCCTGCTTTGTCAGTGTGTCCGGttt                                  >  1:1896046/1‑44 (MQ=255)
                                                    aaGCAACAAGGTTGTACCCTGCTTTGTCAGTGTGTCCGGttt                                  >  1:2119837/1‑42 (MQ=255)
                                                        aacaaGGTTGTAACCTGCTTTGTCAGTGTGTCCGGTTTTGATGCCGTCGACAtt                  <  1:2788560/54‑1 (MQ=255)
                                                        aacaaGGTTGTAACCTGCTTTGTCAGTGTGTCCGGTTTTGATGCCGTCGACAtt                  <  1:244689/54‑1 (MQ=255)
                                                        aacaaGGTTGTAACCTGCTTTGTCAGTGTGTCCGGTTTTGATGCCGTCGACAtt                  <  1:1948480/54‑1 (MQ=255)
                                                        aacaaGGTTGTAACCTGCTTTGTCAGTGTGTCCGGTTTTGATGCCGTCGACAtt                  <  1:679542/54‑1 (MQ=255)
                                                        aacaaGGTTGTAACCTGCTTTGTCAGTGTGTCCGGTTTTGATGCCGTCGACAtt                  <  1:1206042/54‑1 (MQ=255)
                                                        aacaaGGTTGTAACCTGCTTTGTCAGTGTGTCCGGTTTTGATGCCGTCGACAtt                  <  1:600559/54‑1 (MQ=255)
                                                        aacaaGGTTGTAACCTGCTTTGTCAGTGTGTCCGGTTTTGATGCCGTCGACAtt                  <  1:2949233/54‑1 (MQ=255)
                                                        aacaaGGTTGTAACCTGCTTTGTCAGTGTGTCCGGTTTTGATGCCGTCGACAtt                  <  1:3341413/54‑1 (MQ=255)
                                                        aacaaGGTTGTAACCTGCTTTGTCAGTGTGTCCGGTTTTGATGCCGTCGACAtt                  <  1:3248728/54‑1 (MQ=255)
                                                         acaaGGTTGTAACCTGCTTTGTCAGTGTGTCCGGTTTTGATGCCGTCGACATTCAGGCTGTTATCCCAt  <  1:1161879/69‑1 (MQ=255)
                                                         acaaGGTTGTAACCTGCTTTGTCAGTGTGTCCGGTTTTGATGCCGTCGACATTCAGGCTGTTATCCCAt  <  1:938664/69‑1 (MQ=255)
                                                         acaaGGTTGTAACCTGCTTTGTCAGTGTGTCCGGTTTTGATGCCGTCGACATTCAGGCTGTTATCCCAt  <  1:815930/69‑1 (MQ=255)
                                                         acaaGGTTGTAACCTGCTTTGTCAGTGTGTCCGGTTTTGATGCCGTCGACATTCAGGCTGTTATCCCAt  <  1:1508197/69‑1 (MQ=255)
                                                         acaaGGTTGTAACCTGCTTTGTCAGTGTGTCCGGTTTTGATGCCGTCGACATTCAGGCTGTTATCCCAt  <  1:3032462/69‑1 (MQ=255)
                                                         acaaGGTTGTAACCTGCTTTGTCAGTGTGTCCGGTTTTGATGCCGTCGACATTCAGGCTGTTATCCCAt  <  1:2995423/69‑1 (MQ=255)
                                                              gTTGTAACCTGCTTTGTCAGTGTGTCCGGTTTTGATGCCGTCGACATTCAGGCTGTTATCCCAt  <  1:847244/64‑1 (MQ=255)
                                                                    |                                                         
GTACGTCCGCCCATTACCGCAGAAATCAAGCGCATCTGGCCTTCAGTCGCAGAAGCAACAAGGTTGTAACCTGCTTTGTCAGTGTGTCCGGTTTTGATGCCGTCGACATTCAGGCTGTTATCCCAT  >  minE/400718‑400843

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