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 443,087 T→C 30.4% K225K (AAA→AAG)  speF ← ornithine decarboxylase isozyme, inducible

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE443,0870TC30.4% 83.7 / 43.6 92K225K (AAA→AAG) speFornithine decarboxylase isozyme, inducible
Reads supporting (aligned to +/- strand):  ref base T (25/39);  new base C (12/16);  total (37/55)
Fisher's exact test for biased strand distribution p-value = 8.19e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACGTGCCGTTTCCAGATAAACCGGTGTTGCACCAGCCTGTAGCAACGCTCCGTGGTGGTTAGATTTGTGGTTATTGCGATCAAACAGCACCAGATCACCCGGTGTTAGCAGGGCGTTTAAAACCACTTT  >  minE/443024‑443152
                                                               |                                                                 
aCGTGCCGTTTCCAGATAAACCGGTGTTGCACCAGCCTGTAGCAACGCTCCGTGGTGGTTAGATTtgtg                                                              >  1:998460/1‑69 (MQ=255)
aCGTGCCGTTTCCAGATAAACCGGTGTTGCACCAGCCTGTAGCAACGCTCCGTGGTGGTTAGATTtgtg                                                              >  1:2288346/1‑69 (MQ=255)
aCGTGCCGTTTCCAGATAAACCGGTGTTGCACCAGCCTGTAGCAACGCTCCGTGGTGGTTAGATTtgtg                                                              >  1:560607/1‑69 (MQ=255)
aCGTGCCGTTTCCAGATAAACCGGTGTTGCACCAGCCTGTAGCAACGCTCCGTGGTGGTTAGATTtgtg                                                              >  1:2050068/1‑69 (MQ=255)
aCGTGCCGTTTCCAGATAAACCGGTGTTGCACCAGCCTGTAGCAACGCTCCGTGGTGGTTAGATTtgtg                                                              >  1:1573200/1‑69 (MQ=255)
aCGTGCCGTTTCCAGATAAACCGGTGTTGCACCAGCCTGTAGCAACGCTCCGTGGTGGTTAGATTtgtg                                                              >  1:1963643/1‑69 (MQ=255)
aCGTGCCGTTTCCAGATAAACCGGTGTTGCACCAGCCTGTAGCAACGCTCCGTGGTGGTTAGATTtgtg                                                              >  1:1324708/1‑69 (MQ=255)
aCGTGCCGTTTCCAGATAAACCGGTGTTGCACCAGCCTGTAGCAACGCTCCGTGGTGGTTAGATTtgtg                                                              >  1:2636865/1‑69 (MQ=255)
   tGCCGTTTCCAGATAAACCGGTGTTGCACCAGCCTGTAGCAACGCTCCGTGGTGGTTAGATTTGTGGt                                                            <  1:1817336/68‑1 (MQ=255)
   tGCCGTTTCCAGATAAACCGGTGTTGCACCAGCCTGTAGCAACGCTCCGTGGTGGTTAGATTTGTGGt                                                            <  1:444477/68‑1 (MQ=255)
   tGCCGTTTCCAGATAAACCGGTGTTGCACCAGCCTGTAGCAACGCTCCGTGGTGGTTAGATTTGTGGt                                                            <  1:3142555/68‑1 (MQ=255)
   tGCCGTTTCCAGATAAACCGGTGTTGCACCAGCCTGTAGCAACGCTCCGTGGTGGTTAGATTTGTGGt                                                            <  1:2379398/68‑1 (MQ=255)
   tGCCGTTTCCAGATAAACCGGTGTTGCACCAGCCTGTAGCAACGCTCCGTGGTGGTTAGATTTGTGGt                                                            <  1:94840/68‑1 (MQ=255)
   tGCCGTTTCCAGATAAACCGGTGTTGCACCAGCCTGTAGCAACGCTCCGTGGTGGTTAGATTTGTGGt                                                            <  1:973513/68‑1 (MQ=255)
   tGCCGTTTCCAGATAAACCGGTGTTGCACCAGCCTGTAGCAACGCTCCGTGGTGGTTAGATTTGTGGt                                                            <  1:1186198/68‑1 (MQ=255)
              gATAAACCGGTGTTGCACCAGCCTGTAGCAACGCTCCGTGGTGGTTAGATTTGTGGTTATTGCGATCa                                                 <  1:846597/68‑1 (MQ=255)
              gATAAACCGGTGTTGCACCAGCCTGTAGCAACGCTCCGTGGTGGTTAGATTTGTGGTTATTGCGATCa                                                 <  1:3060119/68‑1 (MQ=255)
              gATAAACCGGTGTTGCACCAGCCTGTAGCAACGCTCCGTGGTGGTTAGATTTGTGGTTATTGCGATCa                                                 <  1:775330/68‑1 (MQ=255)
              gATAAACCGGTGTTGCACCAGCCTGTAGCAACGCTCCGTGGTGGTTAGATTTGTGGTTATTGCGATCa                                                 <  1:450607/68‑1 (MQ=255)
                  aaCCGGTGTTGCACCAGCCTGTAGCAACGCTCCGTGGTGGTTAGATTTGTGGTTATTGCGATCAAACAg                                            <  1:2594016/69‑1 (MQ=255)
                     cGGTGTTGCACCAGCCTGTAGCAACGCTCCGTGGTGGTTAGATTTGTGGTTATTGCGATCAAACAGCAc                                         <  1:1557978/69‑1 (MQ=255)
                     cGGTGTTGCACCAGCCTGTAGCAACGCTCCGTGGTGGTTAGATTTGTGGTTATTGCGATCAAACAGCAc                                         <  1:33549/69‑1 (MQ=255)
                     cGGTGTTGCACCAGCCTGTAGCAACGCTCCGTGGTGGTTAGATTTGTGGTTATTGCGATCAAACAGCAc                                         <  1:1307233/69‑1 (MQ=255)
                     cGGTGTTGCACCAGCCTGTAGCAACGCTCCGTGGTGGTTAGATTTGTGGTTATTGCGATCAAACAGCAc                                         <  1:1288985/69‑1 (MQ=255)
                     cGGTGTTGCACCAGCCTGTAGCAACGCTCCGTGGTGGTTAGATTTGTGGTTATTGCGATCAAACAGCAc                                         <  1:1351968/69‑1 (MQ=255)
                        tgtTGCACCAGCCTGTAGCAACGCTCCGTGGTGGTTAGATTTGTGGTTATTGCGATCAAACAGCACCAg                                      <  1:1250871/69‑1 (MQ=255)
                        tgtTGCACCAGCCTGTAGCAACGCTCCGTGGTGGTTAGATTTGTGGTTATTGCGATCAAACAGCACCAg                                      <  1:3196500/69‑1 (MQ=255)
                        tgtTGCACCAGCCTGTAGCAACGCTCCGTGGTGGTTAGATTTGTGGTTATTGCGATCAAACAGCACCAg                                      <  1:1629994/69‑1 (MQ=255)
                        tgtTGCACCAGCCTGTAGCAACGCTCCGTGGTGGTTAGATTTGTGGTTATTGCGATCAAACAGCACCAg                                      <  1:1397264/69‑1 (MQ=255)
                        tgtTGCACCAGCCTGTAGCAACGCTCCGTGGTGGTTAGATTTGTGGTTATTGCGATCAAACAGCACCAg                                      <  1:1432922/69‑1 (MQ=255)
                        tgtTGCACCAGCCTGTAGCAACGCTCCGTGGTGGTTAGATTTGTGGTTATTGCGATCAAACAGCACCAg                                      <  1:1538942/69‑1 (MQ=255)
                            gCACCAGCCTGTAGCAACGCTCCGTGGTGGTTAGATTTGTGGTTATTGCGATCAAACAGCACCAGATCa                                  <  1:1935833/69‑1 (MQ=255)
                            gCACCAGCCTGTAGCAACGCTCCGTGGTGGTTAGATTTGTGGTTATTGCGATCAAACAGCACCAGATCa                                  <  1:3368711/69‑1 (MQ=255)
                            gCACCAGCCTGTAGCAACGCTCCGTGGTGGTTAGATTTGTGGTTATTGCGATCAAACAGCACCAGATCa                                  <  1:2839725/69‑1 (MQ=255)
                                 aGCCTGTAGCAAGGCCCCGTGATGGTTAGACTTATGGTTATTGCGGTCaaa                                               >  1:126581/1‑51 (MQ=16)
                                 aGCCTGTAGCAAGGCCCCGTGATGGTTAGACTTATGGTTATTGCGGTCAAACAGCACCAGATCACCCgg                             >  1:2305584/1‑69 (MQ=255)
                                 aGCCTGTAGCAAGGCCCCGTGATGGTTAGACTTATGGTTATTGCGGTCAAACAGCACCAGATCACCCgg                             >  1:2204787/1‑69 (MQ=255)
                                 aGCCTGTAGCAAGGCCCCGTGATGGTTAGACTTATGGTTATTGCGGTCAAACAGCACCAGATCACCCgg                             >  1:871370/1‑69 (MQ=255)
                                 aGCCTGTAGCAAGGCCCCGTGATGGTTAGACTTATGGTTATTGCGGTCAAACAGCACCAGATCACCCgg                             >  1:1138344/1‑69 (MQ=255)
                                 aGCCTGTAGCAAGGCCCCGTGATGGTTAGACTTATGGTTATTGCGGTCAAACAGCACCAGATCACCCgg                             >  1:2931605/1‑69 (MQ=255)
                                 aGCCTGTAGCAAGGCCCCGTGATGGTTAGACTTATGGTTATTGCGGTCAAACAGCACCAGATCACCCgg                             >  1:1320430/1‑69 (MQ=255)
                                 aGCCTGTAGCAAGGCCCCGTGATGGTTAGACTTATGGTTATTGCGGTCAAACAGCACCAGATCACCCgg                             >  1:6258/1‑69 (MQ=255)
                                 aGCCTGTAGCAAGGCCCCGTGATGGTTAGACTTATGGTTATTGCGGTCAAACAGCACCAGATCACCCgg                             >  1:1635468/1‑69 (MQ=255)
                                 aGCCTGTAGCAAGGCCCCGTGATGGTTAGACTTATGGTTATTGCGGTCAAACAGCACCAGATCACCCgg                             >  1:1599994/1‑69 (MQ=255)
                                 aGCCTGTAGCAAGGCCCCGTGATGGTTAGACTTATGGTTATTGCGGTCAAACAGCACCAGATCACCCg                              >  1:1756972/1‑68 (MQ=255)
                                 aGCCTGTAGCAAGGCCCCGTGATGGTTAGACTTATGGTTATTGCGGTCAAACAGCACCAGATCACCCg                              >  1:1228621/1‑68 (MQ=255)
                                 aGCCTGTAGCAACGCTCCGTGGTGGTTAGATTTGTGGTTATTGCGATCAAACAGCACCAGATCACCCgg                             >  1:2301586/1‑69 (MQ=255)
                                     tGTAGCAACGCTCCGTGGTGGTTAGATTTGTGGTTATTGCGATCAAACAGCACCAGATCACCCGGTGtt                         <  1:3332181/69‑1 (MQ=255)
                                     tGTAGCAACGCTCCGTGGTGGTTAGATTTGTGGTTATTGCGATCAAACAGCACCAGATCACCCGGTGtt                         <  1:1138232/69‑1 (MQ=255)
                                     tGTAGCAACGCTCCGTGGTGGTTAGATTTGTGGTTATTGCGATCAAACAGCACCAGATCACCCGGTGtt                         <  1:484779/69‑1 (MQ=255)
                                     tGTAGCAACGCTCCGTGGTGGTTAGATTTGTGGTTATTGCGATCAAACAGCACCAGATCACCCGGTGtt                         <  1:2002269/69‑1 (MQ=255)
                                     tGTAGCAACGCTCCGTGGTGGTTAGATTTGTGGTTATTGCGATCAAACAGCACCAGATCACCCGGTGtt                         <  1:1359185/69‑1 (MQ=255)
                                     tGTAGCAACGCTCCGTGGTGGTTAGATTTGTGGTTATTGCGATCAAACAGCACCAGATCACCCGGTGtt                         <  1:1913874/69‑1 (MQ=255)
                                     tGTAGCAACGCTCCGTGGTGGTTAGATTTGTGGTTATTGCGATCAAACAGCACCAGATCACCCGGTGtt                         <  1:1549524/69‑1 (MQ=255)
                                     tGTAGCAACGCTCCGTGGTGGTTAGATTTGTGGTTATTGCGATCAAACAGCACCAGATCACCCGGTGtt                         <  1:1789373/69‑1 (MQ=255)
                                      gTAGCAACGCTCCGTGGTGGTTAGATTTGTGGTTATTGCGATCAAACAGCACCAGATCACCCGGTGtt                         <  1:1333217/68‑1 (MQ=255)
                                      gTAGCAACGCTCCGTGGTGGTTAGATTTGTGGTTATTGCGATCAAACAGCACCAGATCACCCGGTGtt                         <  1:1483034/68‑1 (MQ=255)
                                         gCAACGCTCCGTGGTGGTTAGATTTGTGGTTATTGCGATCAAACAGCACCAg                                      >  1:1704637/1‑52 (MQ=255)
                                         gCAACGCTCCGTGGTGGTTAGATTTGTGGTTATTGCGATCAAACAGCACCAg                                      >  1:3109506/1‑52 (MQ=255)
                                         gCAACGCTCCGTGGTGGTTAGATTTGTGGTTATTGCGATCAAACAGCACCAg                                      >  1:3058965/1‑52 (MQ=255)
                                         gCAACGCTCCGTGGTGGTTAGATTTGTGGTTATTGCGATCAAACAGCACCAg                                      >  1:302453/1‑52 (MQ=255)
                                         gCAACGCTCCGTGGTGGTTAGATTTGTGGTTATTGCGATCAAACAGCACCAg                                      >  1:3436444/1‑52 (MQ=255)
                                         gCAACGCTCCGTGGTGGTTAGATTTGTGGTTATTGCGATCAAACAGCACCAg                                      >  1:903819/1‑52 (MQ=255)
                                         gCAACGCTCCGTGGTGGTTAGATTTGTGGTTATTGCGATCAAACAGCACCAg                                      >  1:1104884/1‑52 (MQ=255)
                                         gCAACGATCCGTGGTGGTTAGATTTGTGGTTATTGCGATCAAACAGCACCAg                                      >  1:436860/1‑52 (MQ=255)
                                           aaCGCTCCGTGGTGGTTAGATTTGTGGTTATTGCGATCAAACAGCAc                                         <  1:1753322/47‑1 (MQ=255)
                                           aaCGCTCCGTGGTGGTTAGATTTGTGGTTATTGCGATCAAACAGCACCAGATCACCCGGTGTTAGCAg                    <  1:2290067/68‑1 (MQ=255)
                                                  cGTGATGGTTAGACTTATGGTTATTGCGGTCAAACAGCACCAGATCACCCGGTGTCAGCAGGGCGTTTa            <  1:1730427/69‑1 (MQ=255)
                                                  cGTGATGGTTAGACTTATGGTTATTGCGGTCAAACAGCACCAGATCACCCGGTGTCAGCAGGGCGTTTa            <  1:1739126/69‑1 (MQ=255)
                                                  cGTGATGGTTAGACTTATGGTTATTGCGGTCAAACAGCACCAGATCACCCGGTGTCAGCAGGGCGTTTa            <  1:333231/69‑1 (MQ=255)
                                                  cGTGATGGTTAGACTTATGGTTATTGCGGTCAAACAGCACCAGATCACCCGGTGTCAGCAGGGCGTTTa            <  1:1657319/69‑1 (MQ=255)
                                                  cGTGATGGTTAGACTTATGGTTATTGCGGTCAAACAGCACCAGATCACCCGGTGTCAGCAGGGCGTTTa            <  1:1200419/69‑1 (MQ=255)
                                                  cGTGATGGTTAGACTTATGGTTATTGCGGTCAAACAGCACCAGATCACCCGGTGTCAGCAGGGCGTTTa            <  1:882560/69‑1 (MQ=255)
                                                  cGTGATGGTTAGACTTATGGTTATTGCGGTCAAACAGCACCAGATCACCCGGTGTCAGCAGGGCGTTTa            <  1:2882999/69‑1 (MQ=255)
                                                  cGTGATGGTTAGACTTATGGTTATTGCGGTCAAACAGCACCAGATCACCCGGTGTCAGCAGGGCGTTTa            <  1:1840495/69‑1 (MQ=255)
                                                  cGTGATGGTTAGACTTATGGTTATTGCGGTCAAACAGCACCAGATCACCCGGTGTCAGCAGGGCGTTTa            <  1:1511786/69‑1 (MQ=255)
                                                  cGTGATGGTTAGACTTATGGTTATTGCGGTCAAACAGCACCAGATCACCCGGTGTCAGCAGGGCGTTTa            <  1:1909539/69‑1 (MQ=255)
                                                  cGTGATGGTTAGACTTATGGTTATTGCGGTCAAACAGCACCAGATCACCCGGTGTCAGCAGGGCGTTTa            <  1:1309120/69‑1 (MQ=255)
                                                  cGTGATGGTTAGACTTATGGTTATTGCGGTCAAACAGCACCAGATCACCCGGTGTCAGCAGGGCGTTTa            <  1:2012926/69‑1 (MQ=255)
                                                  cGTGATGGTTAGACTTATGGTTATTGCGGTCAAACAGCACCAGATCACCCGGTGTCAGCAGGGCGTTTa            <  1:562897/69‑1 (MQ=255)
                                                  cGTGATGGTTAGACTTATGGTTATTGCGGTCAAACAGCACCAGATCACCCGGTGTCAGCAGGGCGTTTa            <  1:2549878/69‑1 (MQ=255)
                                                  cGTGATGGTTAGACTTATGGTTATTGCGGTCAAACAGCACCAGATCACCCGGTGTCAGCAGGGCGTTTa            <  1:766320/69‑1 (MQ=255)
                                                   gtgatgGTTAGACTTATGGTTATTGCGGTCAAACAGCACCAGATCACCCGGTGTCAGCAGGGCGTTTa            <  1:1423889/68‑1 (MQ=255)
                                                     ggtggtTAGATTTGTGGTTATTGCGATCAAACAGCAc                                         <  1:2023769/37‑1 (MQ=255)
                                                            aGATTTGTGGTTATTGCGATCAAACAGCACCAGATCACCCGGTGTTAGCAGGGCGt               >  1:2056042/1‑56 (MQ=255)
                                                            aGATTTGTGGTTATTGCGATCAAACAGCACCAGATCACCCGGTGTTAGCAGGGCGTTTAAAACCACttt  >  1:723238/1‑69 (MQ=255)
                                                            aGATTTGTGGTTATTGCGATCAAACAGCACCAGATCACCCGGTGTTAGCAGGGCGTTTAAAACCACttt  >  1:314529/1‑69 (MQ=255)
                                                            aGATTTGTGGTTATTGCGATCAAACAGCACCAGATCACCCGGTGTTAGCAGGGCGTTTAAAACCACttt  >  1:534263/1‑69 (MQ=255)
                                                            aGATTTGTGGTTATTGCGATCAAACAGCACCAGATCACCCGGTGTTAGCAGGGCGTTTAAAACCACttt  >  1:1259871/1‑69 (MQ=255)
                                                            aGATTTGTGGTTATTGCGATCAAACAGCACCAGATCACCCGGTGTTAGCAGGGCGTTTAAAACCACttt  >  1:2977850/1‑69 (MQ=255)
                                                            aGATTTGTGGTTATTGCGATCAAACAGCACCAGATCACCCGGTGTTAGCAGGGCGTTTAAAACCACttt  >  1:1234141/1‑69 (MQ=255)
                                                            aGATTTGTGGTTATTGCGATCAAACAGCACCAGATCACCCGGTGTTAGCAGGGCGTTTAAAACCACttt  >  1:1566651/1‑69 (MQ=255)
                                                               |                                                                 
ACGTGCCGTTTCCAGATAAACCGGTGTTGCACCAGCCTGTAGCAACGCTCCGTGGTGGTTAGATTTGTGGTTATTGCGATCAAACAGCACCAGATCACCCGGTGTTAGCAGGGCGTTTAAAACCACTTT  >  minE/443024‑443152

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