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 1,347,113 A→G 26.8% A202A (GCA→GCG)  yegH → fused predicted membrane proteins

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,347,1130AG26.8% 70.8 / 25.3 67A202A (GCA→GCG) yegHfused predicted membrane proteins
Reads supporting (aligned to +/- strand):  ref base A (38/11);  new base G (4/14);  total (42/25)
Fisher's exact test for biased strand distribution p-value = 9.52e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GATCGTTATTCTCTGCTTAAGCTTCCTGTTGATGATTGGCTTTAGCCTGGTGGCAGAAGGTTTCGGCTTCGTCATTCCGAAAGGCTACCTGTACGCTGCCATTGGTTTCTCGGTGATG  >  minE/1347059‑1347176
                                                      |                                                               
gaTCGTTATTCTCTGCTTAAGCTTCCTGTTGATGATTGGCTTTAGCCTGGTGGCAGAAGGTTTCGGCtt                                                   >  1:2008452/1‑69 (MQ=255)
 aTCGTTATTCTCTTCTTAAGCTTCCTGTTGATGATTGGCTTTAGCCTGGTGGCGGAAGGTTTCGGCTTc                                                  <  1:3393353/69‑1 (MQ=255)
 aTCGTTATTCTCTGCTTAAGCTTCCTGTTGATGATTGGCTTTAGCCTGGTGGCGGAAGGTTTCGGCTTc                                                  <  1:2935949/69‑1 (MQ=255)
 aTCGTTATTCTCTGCTTAAGCTTCCTGTTGATGATTGGCTTTAGCCTGGTGGCGGAAGGTTTCGGCTTc                                                  <  1:1502533/69‑1 (MQ=255)
 aTCGTTATTCTCTGCTTAAGCTTCCTGTTGATGATTGGCTTTAGCCTGGTGGCGGAAGGTTTCGGCTTc                                                  <  1:1548664/69‑1 (MQ=255)
 aTCGTTATTCTCTGCTTAAGCTTCCTGTTGATGATTGGCTTTAGCCTGGTGGCGGAAGGTTTCGGCTTc                                                  <  1:3311159/69‑1 (MQ=255)
 aTCGTTATTCTCTGCTTAAGCTTCCTGTTGATGATTGGCTTTAGCCTGGTGGCGGAAGGTTTCGGCTTc                                                  <  1:3361496/69‑1 (MQ=255)
 aTCGTTATTCTCTGCTTAAGCTTCCTGTTGATGATTGGCTTTAGCCTGGTGGCGGAAGGTTTCGGCTTc                                                  <  1:2450596/69‑1 (MQ=255)
 aTCGTTATTCTCTGCTTAAGCTTCCTGTTGATGATTGGCTTTAGCCTGGTGGCGGAAGGTTTCGGCTTc                                                  <  1:2443149/69‑1 (MQ=255)
 aTCGTTATTCTCTGCTTAAGCTTCCTGTTGATGATTGGCTTTAGCCTGGTGGCGGAAGGTTTCGGCTTc                                                  <  1:1963192/69‑1 (MQ=255)
 aTCGTTATTCTCTGCTTAAGCTTCCTGTTGATGATTGGCTTTAGCCTGGTGGCGGAAGGTTTCGGCTTc                                                  <  1:1241989/69‑1 (MQ=255)
 aTCGTTATTCTCTGCTTAAGCTTCCTGTTGATGATTGGCTTTAGCCTGGTGGCGGAAGGTTTCGGCTTc                                                  <  1:753634/69‑1 (MQ=255)
   cGTTATTCTCTGCTTAAGCTTCCTGTTGATGATTGGCTTTAGCCTGGTGGCAGAAGGt                                                           >  1:1974820/1‑58 (MQ=255)
   cGTTATTCTCTGCTTAAGCTTCCTGTTGATGATTGGCTTTAGCCTGGTGGCAGAAGGt                                                           >  1:2809764/1‑58 (MQ=255)
   cGTTATTCTCTGCTTAAGCTTCCTGTTGATGATTGGCTTTAGCCTGGTGGCAGAAGGt                                                           >  1:2091903/1‑58 (MQ=255)
   cGTTATTCTCTGCTTAAGCTTCCTGTTGATGATTGGCTTTAGCCTGGTGGCAGAAGGt                                                           >  1:2315473/1‑58 (MQ=255)
   cGTTATTCTCTGCTTAAGCTTCCTGTTGATGATTGGCTTTAGCCTGGTGGCAGAAGGt                                                           >  1:3131553/1‑58 (MQ=255)
       aTTCTCTGCTTAAGCTTCCTGTTGATGATTGGCTTTAGCCTGGTGGCAGAAGGt                                                           >  1:3384616/1‑54 (MQ=255)
       aTTCTCTGCTTAAGCTTCCTGTTGATGATTGGCTTTAGCCTGGTGGCAGAAGGt                                                           >  1:651517/1‑54 (MQ=255)
       aTTCTCTGCTTAAGCTTCCTGTTGATGATTGGCTTTAGCCTGGTGGCAGAAGGt                                                           >  1:1193088/1‑54 (MQ=255)
       aTTCTCTGCTTAAGCTTCCTGTTGATGATTGGCTTTAGCCTGGTGGCAGAAGGt                                                           >  1:1998525/1‑54 (MQ=255)
       aTTCTCTGCTTAAGCTTCCTGTTGATGATTGGCTTTAGCCTGGTGGCAGAAGGTTTCGGCTTCGt                                                <  1:3216625/65‑1 (MQ=255)
       aTTCTCTGCTTAAGCTTCCTGTTGATGATTGGCTTTAGCCTGGTGGCAGAAGGTTTCGGCTTCGt                                                <  1:1970479/65‑1 (MQ=255)
             tGCTTAAGCTTCCTGTTGATGATTGGCTTTAGCCTGGTGGCGGAAGGTTTCGGCTTc                                                  <  1:1385201/57‑1 (MQ=255)
                 tAAGCTTCCTGTTGATGATTGGCTTTAGCCTGGTGGCAGAAgg                                                            >  1:697213/1‑43 (MQ=255)
                 tAAGCTTCCTGTTGATGATTGGCTTTAGCCTGGTGGCAGAAgg                                                            >  1:1103642/1‑43 (MQ=255)
                 tAAGCTTCCTGTTGATGATTGGCTTTAGCCTGGTGGCAGAAgg                                                            >  1:1137503/1‑43 (MQ=255)
                 tAAGCTTCCTGTTGATGATTGGCTTTAGCCTGGTGGCAGAAGGTTTCGGCTTCGTCATTCCGAAAGGCt                                  <  1:91591/69‑1 (MQ=255)
                 tAAGCTTCCTGTTGATGATTGGCTTTAGCCTGGTGGCAGAAGGTTTCGGCTTCGTCATTCCGAAAGGCt                                  <  1:2484366/69‑1 (MQ=255)
                     cTTCCTGTTGATGATTGGCTTTAGCCTGGTGGCGGATGGTTTCGGCTTc                                                  <  1:862081/49‑1 (MQ=38)
                              gatgatTGGCTTTAGCCTGGTGGCAGAAGGTTTCGGc                                                     >  1:2216821/1‑37 (MQ=255)
                              gatgatTGGCTTTAGCCTGGTGGCAGAAGGTTTCGGc                                                     >  1:1184326/1‑37 (MQ=255)
                              gatgatTGGCTTTAGCCTGGTGGCAGAAGGTTTCGGc                                                     >  1:1185000/1‑37 (MQ=255)
                              gatgatTGGCTTTAGCCTGGTGGCAGAAGGTTTCGGc                                                     >  1:700481/1‑37 (MQ=255)
                              gatgatTGGCTTTAGCCTGGTGGCAGAAGGTTTCGGc                                                     >  1:1365317/1‑37 (MQ=255)
                              gatgatTGGCTTTAGCCTGGTGGCAGAAGGTTTCGGc                                                     >  1:143648/1‑37 (MQ=255)
                              gatgatTGGCTTTAGCCTGGTGGCAGAAGGTTTCGGc                                                     >  1:2919405/1‑37 (MQ=255)
                              gatgatTGGCTTTAGCCTGGTGGCAGAAGGTTTCGGc                                                     >  1:2900572/1‑37 (MQ=255)
                              gatgatTGGCTTTAGCCTGGTGGCAGAAGGTTTCGGc                                                     >  1:1776763/1‑37 (MQ=255)
                              gatgatTGGCTTTAGCCTGGTGGCAGAAGGTTTCGGc                                                     >  1:2333464/1‑37 (MQ=255)
                              gatgatTGGCTTTAGCCTGGTGGCAGAAGGTTTCGGc                                                     >  1:2613604/1‑37 (MQ=255)
                              gatgatTGGCTTTAGCCTGGTGGCAGAAGGTTTCGGc                                                     >  1:2373319/1‑37 (MQ=255)
                              gatgatTGGCTTTAGCCTGGTGGCAGAAGGTTTCGGc                                                     >  1:188615/1‑37 (MQ=255)
                              gatgatTGGCTTTAGCCTGGTGGCAGAAGGTTTCAGc                                                     >  1:1252202/1‑37 (MQ=255)
                               atgatTGGCTTTAGCCTGGTGGCGGAAGGTTTCGGCTTc                                                  <  1:3015723/39‑1 (MQ=255)
                                          tAGCCTGGTGGCGGAAGGTTTCGGCTTCGTCATTCCGAAAGGCTACCTGTACGCTGCCATTGGTTtctc         >  1:888658/1‑69 (MQ=255)
                                          tAGCCTGGTGGCGGAAGGTTTCGGCTTCGTCATTCCGAAAGGCTACCTGTACGCTGCCATTGGTTtctc         >  1:633052/1‑69 (MQ=255)
                                          tAGCCTGGTGGCGGAAGGTTTCGGCTTCGTCATTCCGAAAGGCTACCTGTACGCTGCCATTGGTTtctc         >  1:1487984/1‑69 (MQ=255)
                                          tAGCCTGGTGGCGGAAGGTTTCGGCTTCGTCATTCCGAAAGGCTACCTGTACGCTGCCATTGGTTtctc         >  1:335759/1‑69 (MQ=255)
                                            gCCTGGTGGCAGAAGGTTTCGGCTTCGTCATTCCGAAAGGCTACCTGTACGCTGCCATTGGTTTCTCg        >  1:2663809/1‑68 (MQ=255)
                                            gCCTGGTGGCAGAAGGTTTCGGCTTCGTCATTCCGAAAGGCTACCTGTACGCTGCCATTGGTTTCTCg        >  1:404474/1‑68 (MQ=255)
                                             ccTGGTGGCAGAAGGTTTCGGCTTCGTCATTCCGCAAGGCTACCTGTACGCTGCCATTGGTTTCTCg        >  1:316678/1‑67 (MQ=255)
                                             ccTGGTGGCAGAAGGTTTCGGCTTCGTCATTCCGAAAGGc                                   >  1:2099097/1‑40 (MQ=255)
                                             ccTGGTGGCAGAAGGTTTCGGCTTCGTCATTCCGAAAGGCTACCTGTACGCTGCCATTGGTTTCTCg        >  1:1272550/1‑67 (MQ=255)
                                             ccTGGTGGCAGAAGGTTTCGGCTTCGTCATTCCGAAAGGCTACCTGTACGCTGCCATTGGTTTCTCg        >  1:3165279/1‑67 (MQ=255)
                                             ccTGGTGGCAGAAGGTTTCGGCTTCGTCATTCCGAAAGGCTACCTGTACGCTGCCATTGGTTTCTCg        >  1:460891/1‑67 (MQ=255)
                                             ccTGGTGGCAGAAGGTTTCGGCTTCGTCATTCCGAAAGGCTACCTGTACGCTGCCATTGGTTTCTCg        >  1:1511120/1‑67 (MQ=255)
                                             ccTGGTGGCAGAAGGTTTCGGCTTCGTCATTCCGAAAGGCTACCTGTACGCTGCCATTGGTTTCTCg        >  1:2752307/1‑67 (MQ=255)
                                             ccTGGTGGCAGAAGGTTTCGGCTTCGTCATTCCGAAAGGCTACCTGTACGCTGCCATTGGTTTCTCg        >  1:2615893/1‑67 (MQ=255)
                                             catggtggCAGAAGGTTTCGGCTTCGTCATTCCGAAAGGCTACCTGt                            >  1:1188763/3‑47 (MQ=255)
                                                   ggCAGAAGGTTTCGGCTTCGTCATTCCGAAAGGCTACCTGTACGCTGCCATTGGTTTCTCGGtgatg  <  1:3285552/67‑1 (MQ=255)
                                                   ggCAGAAGGTTTCGGCTTCGTCATTCCGAAAGGCTACCTGTACGCTGCCATTGGTTTCTCGGtgatg  <  1:1452437/67‑1 (MQ=255)
                                                   ggCAGAAGGTTTCGGCTTCGTCATTCCGAAAGGCTACCTGTACGCTGCCATTGGTTTCTCGGtgatg  <  1:1481876/67‑1 (MQ=255)
                                                   ggCAGAAGGTTTCGGCTTCGTCATTCCGAAAGGCTACCTGTACGCTGCCATTGGTTTCTCGGtgatg  <  1:1877373/67‑1 (MQ=255)
                                                   ggCAGAAGGTTTCGGCTTCGTCATTCCGAAAGGCTACCTGTACGCTGCCATTGGTTTCTCGGtgatg  <  1:2516721/67‑1 (MQ=255)
                                                   ggCAGAAGGTTTCGGCTTCGTCATTCCGAAAGGCTACCTGTACGCTGCCATTGGTTTCTCGGtgatg  <  1:2096721/67‑1 (MQ=255)
                                                    gCAGAAGGTTTCGGCTTCGTCATTCCGAAAGGCTACCTGTACGCTGCCATTGGTTTCTCGGtgatg  <  1:1913711/66‑1 (MQ=255)
                                                      |                                                               
GATCGTTATTCTCTGCTTAAGCTTCCTGTTGATGATTGGCTTTAGCCTGGTGGCAGAAGGTTTCGGCTTCGTCATTCCGAAAGGCTACCTGTACGCTGCCATTGGTTTCTCGGTGATG  >  minE/1347059‑1347176

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