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 F21 I0 R1 2169 63.0 3952800 76.2% 3012033 62.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,015,013 T→C 15.1% K352K (AAA→AAG) ‡ fumA ← aerobic Class I fumarate hydratase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,015,0130TC15.1% 124.2 / 14.4 53K352K (AAA→AAG) ‡fumAaerobic Class I fumarate hydratase
Reads supporting (aligned to +/- strand):  ref base T (24/21);  new base C (3/5);  total (27/26)
Fisher's exact test for biased strand distribution p-value = 4.67e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.98e-01

CGACAACTGTGCGAGGATCTCTTTCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAGATCCCCTGACG  >  minE/1014944‑1015081
                                                                     |                                                                    
cGACAACTGTGCGAGGATCTCTTTCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCtt                                                                     <  1:2638523/71‑1 (MQ=255)
cGACAACTGTGCGAGGATCTCTTTCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCtt                                                                     <  1:493445/71‑1 (MQ=255)
cGACAACTGTGCGAGGATCTCTTTCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCt                                                                      <  1:2675081/70‑1 (MQ=255)
   cAACTGTGCGAGGATCTCTTTCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTgc                                                                  <  1:3780558/71‑1 (MQ=255)
    aaCTGTGCGAGGATCTCTTTCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTgcg                                                                 >  1:387096/1‑71 (MQ=255)
         ggCGAGGATCTCTTTCATCGTGCGGTTAAGGTCAACTTTCACCGCTTCGCCTTCACCGGCCTGGCGCAgt                                                             >  1:2816912/2‑69 (MQ=255)
              ggATCTCTTTCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTcc                                                       <  1:3810923/71‑1 (MQ=255)
              ggATCTCTTTCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCACGCTTTGCGCAGCTCTTcc                                                       >  1:839054/1‑71 (MQ=255)
                aTCTCTTTCATCGGGCGGTTAAGGTCAACTTTCACCGCTTCGCCTTCACCGGCCTGGCGCAGTTCtt                                                         <  1:2651079/67‑1 (MQ=255)
                  ctctTTCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGa                                                   >  1:2393713/1‑71 (MQ=255)
                  ctctTTCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGa                                                   >  1:42080/1‑71 (MQ=255)
                     tttCATCGGACGGTTAAGGTCAACGCCCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGa                                                   <  1:3657820/68‑1 (MQ=255)
                        cATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGatatat                                              <  1:2364981/70‑1 (MQ=255)
                        cATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGa                                                   <  1:2362131/65‑1 (MQ=255)
                           cGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGc                                          >  1:1917220/1‑71 (MQ=255)
                            ggACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGcc                                         >  1:1986686/1‑71 (MQ=255)
                            ggACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGc                                          <  1:150915/70‑1 (MQ=255)
                              aCGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTg                                       <  1:1512345/71‑1 (MQ=255)
                                 gTTAAGGTCAACTTTCACCGCTTCGCCTTCACCGGCCTGGCGCAGTTCTTGTGGAATGTACTGGCCTgggt                                    <  1:1731115/71‑3 (MQ=255)
                                   tAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGatatat                                              >  1:3020890/1‑59 (MQ=255)
                                   tAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTg                                       >  1:1941656/1‑66 (MQ=255)
                                    aaGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATAttt                                            <  1:3523031/60‑1 (MQ=255)
                                    aaGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTAt                                 >  1:1254363/1‑71 (MQ=255)
                                     aGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATg                                >  1:16646/1‑71 (MQ=255)
                                         cAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGtt                              >  1:2462200/1‑69 (MQ=255)
                                          aaCGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGct                                                            >  1:159842/1‑38 (MQ=255)
                                          aaCGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTc                             >  1:2295325/1‑69 (MQ=255)
                                             tttcACCGCTTCGCCTTCACCGGCCTGGCGCAGTTCTTGTGGAATGTACTGGCCTGGGTTGTGTTCCAGtt                        >  1:3721710/4‑71 (MQ=255)
                                              ttcACCGCTTCGCCTTCACCGGCCTGGCGCAGTTCTTGTGGAATGTACTGGCCTGGGTTGTGTTCCAGttt                       >  1:787777/3‑71 (MQ=255)
                                              cgcACCGCTTCGGCTTCTGCCGCTTTTCGCAGCTCTTCCGGGATATATTTGCCTGGATTTTGTTCCAGt                         <  1:2163730/69‑1 (MQ=255)
                                               tcACCGCTTCGCCTTCACCGGCCTGGCGCAGTTCTTGTGGAATGTACTGGCCTGGGTTGTGTTCCAGttt                       <  1:47357/69‑1 (MQ=255)
                                                cACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGttttt                     >  1:2314172/1‑71 (MQ=255)
                                                 aCCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTc                    >  1:3517774/1‑71 (MQ=255)
                                                  ccGCTTCGCCTTCACCGGCCTGGCGCAGTTCTTGTGGAATGTACTGGCCTGGGTTGTGTTCCAGTTTTTCg                   <  1:2290998/71‑1 (MQ=255)
                                                   cGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGa                  <  1:692116/71‑1 (MQ=255)
                                                    gCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATAtt                                             <  1:1404141/43‑1 (MQ=255)
                                                     cTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATc                <  1:437175/71‑1 (MQ=255)
                                                     cTTCGCCTTCACCGGCCTGGCGCAGTTCTTGTGGAATGTACTGGCCTGGGTTGTGTTCCAGttt                       <  1:1406777/64‑1 (MQ=255)
                                                        cGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCa              <  1:1165647/70‑1 (MQ=255)
                                                        cGCCTTCTCCCGCTTTGCCCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCa              <  1:2988440/70‑1 (MQ=255)
                                                          ccTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGt                         <  1:108948/57‑1 (MQ=255)
                                                           cTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAGATc          >  1:1594628/1‑71 (MQ=255)
                                                           cTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAGATc          >  1:1125790/1‑71 (MQ=255)
                                                            ttCTCCCGCTTTGCGCAGCTCTTCCGGGATATAttt                                            <  1:1315451/36‑1 (MQ=255)
                                                            ttCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTTGATTAt                                 <  1:2380/47‑1 (MQ=255)
                                                             tctcCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGt                               >  1:1497999/1‑48 (MQ=255)
                                                              ctcCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAGATc          >  1:3728427/1‑68 (MQ=255)
                                                               tcCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAGAt           >  1:1125932/1‑66 (MQ=255)
                                                               tcCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAGAt           >  1:1121387/1‑66 (MQ=255)
                                                                 ccGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGtt                        <  1:2576907/51‑1 (MQ=255)
                                                                 ccGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAGATCCCCTg     <  1:630993/70‑1 (MQ=255)
                                                                 ccGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAGATCCCCTGa    <  1:1215642/71‑1 (MQ=255)
                                                                   gCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAGATCCCCTGACg  >  1:2947824/1‑71 (MQ=255)
                                                                   gCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAGATCCCCTGACg  >  1:2299975/1‑71 (MQ=255)
                                                                   gCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAGATCCCCTGACg  >  1:1491615/1‑71 (MQ=255)
                                                                    cTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGa                  <  1:3915817/54‑1 (MQ=255)
                                                                     |                                                                    
CGACAACTGTGCGAGGATCTCTTTCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAGATCCCCTGACG  >  minE/1014944‑1015081

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