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 1,841,502 T→C 23.6% E218E (GAA→GAG)  ispD ← 4‑diphosphocytidyl‑2C‑methyl‑D‑erythritol synthase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,841,5020TC23.6% 95.9 / 23.9 76E218E (GAA→GAG) ispD4‑diphosphocytidyl‑2C‑methyl‑D‑erythritol synthase
Reads supporting (aligned to +/- strand):  ref base T (43/15);  new base C (9/9);  total (52/24)
Fisher's exact test for biased strand distribution p-value = 8.07e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CAATTCGCATTATGTATTCTCCTGATGGATGGTTCGGGTGAGGTAAAACTCGGCCAGTGCCAAATCTTCCGGGCGCGTGACTTTAATGTTATCCGCACGGCCTTCGACCAACTGAGGATGGAATCCGCAATAT  >  minE/1841436‑1841568
                                                                  |                                                                  
cAATTCGCATTATGTATTCTCCTGATGGATGGTTCGGGTGAGGTAAAACTCGGCCAGTGCCAAATCt                                                                    >  1:2474971/1‑67 (MQ=255)
cAATTCGCATTATGTATTCTCCTGATGGATGGTTCGGGTGAGGTAAAACTCGGCCAGTGCCAAATCt                                                                    >  1:878949/1‑67 (MQ=255)
cAATTCGCATTATGTATTCTCCTGATGGATGGTTCGGGTGAGGTAAAACTCGGCCAGTGCCAAATCt                                                                    >  1:2777025/1‑67 (MQ=255)
cAATTCGCATTATGTATTCTCCTGATGGATGGTTCGGGTGAGGTAAAACTCGGCCAGTGCCAAATCt                                                                    >  1:840747/1‑67 (MQ=255)
           aTGTATTCTCCTGATGGATGGTTCGGGTGAGGTAAAACTCGGCCAGTGCCAAATCTTCCGGGCGCGTGa                                                       >  1:758886/1‑69 (MQ=255)
           aTGTATTCTCCTGATGGATGGTTCGGGTGAGGTAAAACTCGGCCAGTGCCAAATCTTCCGGGCGCGTGa                                                       >  1:2805568/1‑69 (MQ=255)
           aTGTATTCTCCTGATGGATGGTTCGGGTGAGGTAAAACTCGGCCAGTGCCAAATCTTCCGGGCGCGTGa                                                       >  1:145882/1‑69 (MQ=255)
           aTGTATTCTCCTGATGGATGGTTCGGGTGAGGTAAAACTCGGCCAGTGCCAAATCTTCCGGGCGAGTGa                                                       >  1:630264/1‑69 (MQ=255)
                ttCTCCTGATGGATGGTTCGGGTGAGGTAAAACTCGGCCAGTGCCAAATCTTCCGGGCGCGTGACttt                                                   <  1:861917/68‑1 (MQ=255)
                ttCTCCTGATGGATGGTTCGGGTGAGGTAAAACTCGGCCAGTGCCAAATCTTCCGGGCGCGTGACttt                                                   <  1:2512018/68‑1 (MQ=255)
                ttCTCCTGATGGATGGTTCGGGTGAGGTAAAACTCGGCCAGTGCCAAATCTTCCGGGCGCGTGACttt                                                   <  1:1834461/68‑1 (MQ=255)
                ttCTCCTGATGGATGGTTCGGGTGAGGTAAAACTCGGCCAGTGCCAAATCTTCCGGGCGCGTGACttt                                                   <  1:572033/68‑1 (MQ=255)
                ttCTCCTGATGGATGGTTCGGGTGAGGTAAAACTCGGCCAGTGCCAAATCTTCCGGGCGCGTGACttt                                                   <  1:2762430/68‑1 (MQ=255)
                ttCTCCTGATGGATGGTTCGGGTGAGGTAAAACTCGGCCAGTGCCAAATCTTCCGGGCGCGTGACttt                                                   <  1:2313441/68‑1 (MQ=255)
                ttCTCCTGATGGATGGTTCGGGTGAGGTAAAACTCGGCCAGTGCCAAATCTTCCGGGCGCGTGACttt                                                   <  1:656536/68‑1 (MQ=255)
                ttCTCCTGATGGATGGTTCGGGTGAGGTAAAACTCGGCCAGTGCCAAATCTTCCGGGCGCGTGACttt                                                   <  1:3030428/68‑1 (MQ=255)
                ttCTCCTGATGGATGGTTCGGGTGAGGTAAAACTCGGCCAGTGCCAAATCTTCCGGGCGCGTGACttt                                                   <  1:133869/68‑1 (MQ=255)
                  ctcCTGATGGATGGTTCGGGTGAGGTAAAATTCGGCCAGCGCCAAATCCTCCGGGCGCGTTACcttga                                                 >  1:1222211/1‑66 (MQ=255)
                  ctcCTGATGGATGGTTCGGGTGAGGTAAAATTCGGCCAGCGCCAAATCCTCCGGGCGCGTTACCTTGAt                                                >  1:328644/1‑69 (MQ=255)
                  ctcCTGATGGATGGTTCGGGTGAGGTAAAATTCGGCCAGCGCCAAATCCTCCGGGCGCGTTACCTTGAt                                                >  1:2775300/1‑69 (MQ=255)
                  ctcCTGATGGATGGTTCGGGTGAGGTAAAATTCGGCCAGCGCCAAATCCTCCGGGCGCGTTACCTTGAt                                                >  1:2697066/1‑69 (MQ=255)
                  ctcCTGATGGATGGTTCGGGTGAGGTAAAATTCGGCCAGCGCCAAATCCTCCGGGCGCGTTACCTTGAt                                                >  1:2838479/1‑69 (MQ=255)
                  ctcCTGATGGATGGTTCGGGTGAGGTAAAATTCGGCCAGCGCCAAATCCTCCGGGCGCGTTACCTTGAt                                                >  1:1903170/1‑69 (MQ=255)
                  ctcCTGATGGATGGTTCGGGTGAGGTAAAATTCGGCCAGCGCCAAATCCTCCGGGCGCGTTACCTTGAt                                                >  1:1928250/1‑69 (MQ=255)
                  ctcCTGATGGATGGTTCGGGTGAGGTAAAATTCGGCCAGCGCCAAATCCTCCGGGCGCGTTACCTTGAt                                                >  1:211163/1‑69 (MQ=255)
                  ctcCTGATGGATGGTTCGGGTGAGGTAAAATTCGGCCAGCGCCAAATCCTCCGGGCGCGTTACCTTGAt                                                >  1:520910/1‑69 (MQ=255)
                  ctcCTGATGGATGGTTCGGGTGAGGTAAAACTCGGCCAGTGCCAAATCTTCCGGGCGCGTGACTTTatt                                                >  1:1911508/1‑67 (MQ=255)
                  ctcCTGATGGATGGTTCGGGTGAGGTAAAACTCGGCCAGTGCCAAATCTTCCGGGCGCGTGACTTTAAt                                                >  1:715024/1‑69 (MQ=255)
                  ctcCTGATGGATGGTTCGGGTGAGGTAAAACTCGGCCAGTGCCAAATCTTCCGGGCGCGTGACTTTAAt                                                >  1:2127385/1‑69 (MQ=255)
                  ctcCTGATGGATGGTTCGGGTGAGGTAAAACTCGGCCAGTGCCAAATCTTCCGGGCGCGTGACTTTAAt                                                >  1:1032340/1‑69 (MQ=255)
                  ctcCTGATGGATGGTTCGGGTGAGGTAAAACTCGGCCAGTGCCAAATCTTCCGGGCGCGTGACTTTAAt                                                >  1:2754830/1‑69 (MQ=255)
                  ctcCTGATGGATGGTTCGGGTGAGGTAAAACTCGGCCAGTGCCAAATCTTCCGGGCGCGTGACTTTAAt                                                >  1:1569500/1‑69 (MQ=255)
                  ctcCTGATGGATGGTTCGGGTGAGGTAAAACTCGGCCAGTGCCAAATCTTCCGGGCGCGTGACTTTAAt                                                >  1:1199881/1‑69 (MQ=255)
                       gatggatgGTTCGGGTGAGGTAAAATTCGGCCAGCGCCAAATCCTCCGGGCGCGTTACCTTTATGt                                              <  1:1934872/66‑1 (MQ=255)
                       gatggatgGTTCGGGTGAGGTAAAATTCGGCCAGCGCCAAATCCTCCGGGCGCGTTACCTTGATGt                                              <  1:1118960/66‑1 (MQ=255)
                       gatggatgGTTCGGGTGAGGTAAAATTCGGCCAGCGCCAAATCCTCCGGGCGCGTTACCTTGATGt                                              <  1:2220846/66‑1 (MQ=255)
                       gatggatgGTTCGGGTGAGGTAAAATTCGGCCAGCGCCAAATCCTCCGGGCGCGTTACCTTGATGt                                              <  1:3420620/66‑1 (MQ=255)
                       gatggatgGTTCGGGTGAGGTAAAATTCGGCCAGCGCCAAATCCTCCGGGCGCGTTACCTTGATGt                                              <  1:652165/66‑1 (MQ=255)
                       gatggatgGTTCGGGTGAGGTAAAATTCGGCCAGCGCCAAATCCTCCGGGCGCGTTACCTTGATGt                                              <  1:1629730/66‑1 (MQ=255)
                       gatggatgGTTCGGGTGAGGTAAAATTCGGCCAGCGCCAAATCCTCCGGGCGCGTTACCTTGATGt                                              <  1:173657/66‑1 (MQ=255)
                       gatggatgGTTCGGGTGAGGTAAAATTCGGCCAGCGCCAAATCCTCCGGGCGCGTTACCTTGATGt                                              <  1:695253/66‑1 (MQ=255)
                       gatggatgGTTCGGGTGAGGTAAAATTCGGCCAGCGCCAAATCCTCCGGGCGCGTTACCTTGATGt                                              <  1:1785901/66‑1 (MQ=255)
                       gatggatgGTTCGGGTGAGGTAAAACTCGGCCAGTGCCAAATCTTCCGGGCGCGTGACTTTAATGt                                              <  1:3056518/66‑1 (MQ=255)
                       gatggatgGTTCGGGTGAGGTAAAACTCGGCCAGTGCCAAATCTTCCGGGCGCGTGACTTTAATGt                                              <  1:1416965/66‑1 (MQ=255)
                       gatggatgGTTCGGGTGAGGTAAAACTCGGCCAGTGCCAAATCTTCCGGGCGCGTGACTTTAATGt                                              <  1:1696548/66‑1 (MQ=255)
                             tggTTCGGGTGAGGTAAACCTCGGCCAGTGCCAAATCTTCCGGGCGCGTGACTTTAATGTTATCCGCa                                      >  1:2091343/1‑68 (MQ=255)
                             tggTTCGGGTGAGGTAAAACTCGGCCAGTGCCAAATCTTCCGGGCGCGTGACTTTAATGTTATCCGCa                                      >  1:570844/1‑68 (MQ=255)
                             tggTTCGGGTGAGGTAAAACTCGGCCAGTGCCAAATCTTCCGGGCGCGTGACTTTAATGTTATCCGCAc                                     >  1:2534456/1‑69 (MQ=255)
                             tggTTCGGGTGAGGTAAAACTCGGCCAGTGCCAAATCTTCCGGGCGCGTGACTTTAATGTTATCCGCAc                                     >  1:1759091/1‑69 (MQ=255)
                             tggTTCGGGTGAGGTAAAACTCGGCCAGTGCCAAATCTTCCGGGCGCGTGACTTTAATGTTATCCGCAc                                     >  1:868597/1‑69 (MQ=255)
                                 tCGGGTGAGGTAAAACTCGGCCAGTGCCAAATCTTCCGGGCGCGTGACTTTAATg                                               >  1:323935/1‑55 (MQ=255)
                                 tCGGGTGAGGTAAAACTCGGCCAGTGCCAAATCTTCCGGGCGCGTGACTTTAATGtt                                             >  1:2826722/1‑57 (MQ=255)
                                 tCGGGTGAGGTAAAACTCGGCCAGTGCCAAATCTTCCGGGCGCGTGACTTTAATGtt                                             >  1:2394605/1‑57 (MQ=255)
                                 tCGGGTGAGGTAAAACTCGGCCAGTGCCAAATCTTCCGGGCGCGTGACTTTAATGtt                                             >  1:1269606/1‑57 (MQ=255)
                                            aaaaCTCGGCCAGTGCCAAATCTTCCGGGCGCGTGACTTTAATGTTATCCGCACg                                    >  1:1609878/1‑55 (MQ=255)
                                            aaaaCTCGGCCAGTGCCAAATCTTCCGGGCGCGTGACTTTAATGTTATCCGCACGGCCTTCGACCaa                        >  1:398428/1‑67 (MQ=255)
                                            aaaaCTCGGCCAGTGCCAAATCTTCCGGGCGCGTGACTTTAATGTTATCCGCACGGCCTTCGACCaa                        >  1:3092610/1‑67 (MQ=255)
                                            aaaaCTCGGCCAGTGCCAAATCTTCCGGGCGCGTGACTTTAATGTTATCCGCACGGCCTTCGACCaa                        >  1:2153879/1‑67 (MQ=255)
                                            aaaaCTCGGCCAGTGCCAAATCTTCCGGGCGCGTGACTTTAATGTTATCCGCACGGCCTTCGACCaa                        >  1:824110/1‑67 (MQ=255)
                                            aaaaCTCGGCCAGTGCCAAATCTTCCGGGCGCGTGACTTTAATGTTATCCGCACGGCCTTCGACCaa                        >  1:1534892/1‑67 (MQ=255)
                                            aaaaCTCGGCCAGTGCCAAATCTTCCGGGCGCGTGACTTTAATGTTATCCGCACGGCCGTCGACCaa                        >  1:2112882/1‑67 (MQ=255)
                                                          gCCAAATCTTCCGGGCGCGTGACTTTAATGTTATCCGCTCGGCCTTCGACCAACTGAGGATGGAATcc         >  1:2431269/1‑68 (MQ=255)
                                                          gCCAAATCTTCCGGGCGCGTGACTTTAATGTTATCCGCACGGCCTTCGACCAACTGAGGATGGAATcc         >  1:2415998/1‑68 (MQ=255)
                                                          gCCAAATCTTCCGGGCGCGTGACTTTAATGTTATCCGCACGGCCTTCGACCAACTGAGGATGGAATcc         >  1:1988337/1‑68 (MQ=255)
                                                          gCCAAATCTTCCGGGCGCGTGACTTTAATGTTATCCGCACGGCCTTCGACCAACTGAGGATGGAATcc         >  1:1632459/1‑68 (MQ=255)
                                                           ccAAATCTTCCGGGCGCGTGACTTTAATGTTATCCGCACGGCCTTCGACCAACTg                     >  1:3118545/1‑55 (MQ=255)
                                                           ccAAATCTTCCGGGCGCGTGACTTTAATGTTATCCGCACGGCCTTCGACCAACTg                     >  1:1343376/1‑55 (MQ=255)
                                                           ccAAATCTTCCGGGCGCGTGACTTTAATGTTATCCGCACGGCCTTCGACCAACTGAGGATGGAATCCGc       >  1:1221459/1‑69 (MQ=255)
                                                           ccAAATCTTCCGGGCGCGTGACTTTAATGTTATCCGCACGGCCTTCGACCAACTGAGGATGGAATCCGc       >  1:1595181/1‑69 (MQ=255)
                                                           ccAAATCTTCCGGGCGCGTGACTTTAATGTTATCCGCACGGCCTTCGACCAACTGAGGATGGAATCCGc       >  1:1434185/1‑69 (MQ=255)
                                                              aaTCTTCCGGGCGCGTGACTTTAATGTTATCCGCACGGCCTTCGACCAACTGAGGATGGAATCCGCAat    <  1:2624463/69‑1 (MQ=255)
                                                              aaTCTTCCGGGCGCGTGACTTTAATGTTATCCGCACGGCCTTCGACCAACTGAGGATGGAATCCGCAat    <  1:2141002/69‑1 (MQ=255)
                                                               aTCTTCCGGGCGCGTGACTTTAATGTTATCCGCACGGCCTTCGACCAACTGAGGATGGAATCCGCAata   <  1:2516458/69‑1 (MQ=255)
                                                                tCTTCCGGGCGCGTGACTTTAATGTTATCCGCACGGCCTTCGACCAACTGAGGATGGAATCCGCAatat  >  1:464378/1‑69 (MQ=255)
                                                                tCTTCCGGGCGCGTGACTTTAATGTTATCCGCACGGCCTTCGACCAACTGAGGATGGAATCCGCAatat  >  1:1427505/1‑69 (MQ=255)
                                                                tCTTCCGGGCGCGTGACTTTAATGTTATCCGCACGGCCTTCGACCAACTGAGGATGGAATCCGCAatat  >  1:2206243/1‑69 (MQ=255)
                                                                tCTTCCGGGCGCGTGACTTTAATGTTATCCGCACGGCCTTCGACCAACTGAGGATGGAATCCGCAatat  >  1:287992/1‑69 (MQ=255)
                                                                 cTTCCGGGCGCGTGACTTTAATGTTATCCGCACGGCCTTCGACCAACTGAGGATGGa             >  1:1168806/1‑57 (MQ=255)
                                                                 cTTCCGGGCGCGTGACTTTAATGTTATCCGCACGGCCTTCGACCAACTGAGGATGGAATCCGCAatat  >  1:220520/1‑68 (MQ=255)
                                                                 cTTCCGGGCGCGTGACTTTAATGTTATCCGCACGGCCTTCGACCAACTGAGGATGGAATCCGCAata   >  1:930069/1‑67 (MQ=255)
                                                                  |                                                                  
CAATTCGCATTATGTATTCTCCTGATGGATGGTTCGGGTGAGGTAAAACTCGGCCAGTGCCAAATCTTCCGGGCGCGTGACTTTAATGTTATCCGCACGGCCTTCGACCAACTGAGGATGGAATCCGCAATAT  >  minE/1841436‑1841568

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