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 1,272,913 C→T 55.9% A231A (GCG→GCA)  yedI ← conserved inner membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,272,9130CT55.9% 9.8 / 45.2 59A231A (GCG→GCA) yedIconserved inner membrane protein
Reads supporting (aligned to +/- strand):  ref base C (22/4);  new base T (16/17);  total (38/21)
Fisher's exact test for biased strand distribution p-value = 5.85e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.74e-01

CCATGTACCACAATCCCACCGCCGACGAGGAACATCGCCAGCGTGCCGACAATCGATAACGCTTTCATCAGCCAGGGCGCGATAATCAATAACCCTTTACCTAATGCC  >  minE/1272854‑1272961
                                                           |                                                
ccATGTACCACAATCCCACCGCCGACGAGGAACATCGCCAGCGTGCCGACAATCGATAACGCTTtcatc                                         >  1:95731/1‑69 (MQ=255)
ccATGTACCACAATCCCACCGCCGACGAGGAACATCGCCAGCGTGCCGACAATCGATAACGCTTtcatc                                         >  1:614345/1‑69 (MQ=255)
ccATGTACCACAATCCCACCGCCGACGAGGAACATCGCCAGCGTGCCGACAATCGATAACGCTTtcatc                                         >  1:1202411/1‑69 (MQ=255)
ccATGTACCACAATCCCACCGCCGACGAGGAACATCGCCAGCGTGCCGACAATCGATAACGCTTtcatc                                         >  1:192564/1‑69 (MQ=255)
ccATGTACCACAATCCCACCGCCGACGAGGAACATCGCCAGCGTGCCGACAATCGATAACGCTTtcatc                                         >  1:3219503/1‑69 (MQ=255)
ccATGTACCACAATCCCACCGCCGACGAGGAACATCGCCAGCGTGCCGACAATCGATAACGCTTtcatc                                         >  1:1623245/1‑69 (MQ=255)
ccATGTACCACAATCCCACCGCCGACGAGGAACATCGCCAGCGTGCCGACAATCGATAACGCTTtcatc                                         >  1:1371583/1‑69 (MQ=255)
     tACCACAATCCCACCGCCGACGAGGAACATCGCCAGCGTGCCGACAATCGATAACGCTTTCATCAGc                                      >  1:2074438/1‑67 (MQ=255)
     tACCACAATCCCACCGCCGACGAGGAACATCGCCAGCGTGCCGACAATCGATAACGCTTTCATCAGCCa                                    >  1:1692622/1‑69 (MQ=255)
     tACCACAATCCCACCGCCGACGAGGAACATCGCCAGCGTGCCGACAATCGATAACGCTTTCATCAGCCa                                    >  1:2810769/1‑69 (MQ=255)
     tACCACAATCCCACCGCCGACGAGGAACATCGCCAGCGTGCCGACAATCGATAACGCTTTCATCAGCCa                                    >  1:1725226/1‑69 (MQ=255)
     tACCACAATCCCACCGCCGACGAGGAACATCGCCAGCGTGCCGACAATCGATAACGCTTTCATCAGCCa                                    >  1:3218974/1‑69 (MQ=255)
       ccACAATCCCACCGCCGACGAGGAACATCGCCAGCGTGCCGACAATCGATAACGCTTTCATCAGCCAgg                                  >  1:1266129/1‑69 (MQ=255)
               ccgccgccgACGAGGAACATCGCCAGCGTGCCGACAATCGATAATGCTTTCATCAGCCAGGGCGCGATa                          <  1:2780936/66‑1 (MQ=255)
               ccgccgccgACGAGGAACATCGCCAGCGTGCCGACAATCGATAATGCTTTCATCAGCCAGGGCGCGATa                          <  1:228999/66‑1 (MQ=255)
               ccgccgccgACGAGGAACATCGCCAGCGTGCCGACAATCGATAATGCTTTCATCAGCCAGGGCGCGATa                          <  1:2135441/66‑1 (MQ=255)
               ccgccgccgACGAGGAACATCGCCAGCGTGCCGACAATCGATAATGCTTTCATCAGCCAGGGCGCGATa                          <  1:237691/66‑1 (MQ=255)
               ccgccgccgACGAGGAACATCGCCAGCGTGCCGACAATCGATAATGCTTTCATCAGCCAGGGCGCGATa                          <  1:532120/66‑1 (MQ=255)
               ccgccgccgACGAGGAACATCGCCAGCGTGCCGACAATCGATAATGCTTTCATCAGCCAGGGCGCGATa                          <  1:2463364/66‑1 (MQ=255)
               ccgccgccgACGAGGAACATCGCCAGCGTGCCGACAATCGATAATGCTTTCATCAGCCAGGGCGCGATa                          <  1:3265166/66‑1 (MQ=255)
               ccgccgccgACGAGGAACATCGCCAGCGTGCCGACAATCGATAATGCTTTCATCAGCCAGGGCGCGATa                          <  1:265508/66‑1 (MQ=255)
               ccgccgccgACGAGGAACATCGCCAGCGTGCCGACAATCGATAATGCTTTCATCAGCCAGGGCGCGATa                          <  1:1763100/66‑1 (MQ=255)
               ccgccgccgACGAGGAACATCGCCAGCGTGCCGACAATCGATAATGCTTTCATCAGCCAGGGCGCGATa                          <  1:3060486/66‑1 (MQ=255)
               ccgccgccgACGAGGAACATCGCCAGCGTGCCGACAATCGATAATGCTTTCATCAGCCAGGGCGCGATa                          <  1:2841113/66‑1 (MQ=255)
                    gccgccGAGGAACATCGCCAGCGTGCCGACAATCGATAATGCTTTCATCAGCCAGGGCGCGATAATCa                      >  1:2296519/1‑68 (MQ=255)
                    gccgACGAGGAACATCGCCAGCGTGCCGACAATCGATAATGCTTtcatc                                         >  1:2292638/1‑49 (MQ=255)
                    gccgACGAGGAACATCGCCAGCGTGCCGACAATCGATAATGCTTTCATCAGCCAGGGCGCGATAATc                       >  1:2999945/1‑67 (MQ=255)
                    gccgACGAGGAACATCGCCAGCGTGCCGACAATCGATAATGCTTTCATCAGCCAGGGCGCGATAATCa                      >  1:2814599/1‑68 (MQ=255)
                    gccgACGAGGAACATCGCCAGCGTGCCGACAATCGATAATGCTTTCATCAGCCAGGGCGCGATAATCa                      >  1:1025355/1‑68 (MQ=255)
                    gccgACGAGGAACATCGCCAGCGTGCCGACAATCGATAATGCTTTCATCAGCCAGGGCGCGATAATCa                      >  1:2911899/1‑68 (MQ=255)
                    gccgACGAGGAACATCGCCAGCGTGCCGACAATCGATAATGCTTTCATCAGCCAGGGCGCGATAATCa                      >  1:2148182/1‑68 (MQ=255)
                    gccgACGAGGAACATCGCCAGCGTGCCGACAATCGATAATGCTTTCATCAGCCAGGGCGCGATAATCa                      >  1:1244268/1‑68 (MQ=255)
                    gccgACGAGGAACATCGCCAGCGTGCCGACAATCGATAATGCTTTCATCAGCCAGGGCGCGATAATCa                      >  1:1425847/1‑68 (MQ=255)
                    gccgACGAGGAACATCGCCAGCGTGCCGACAATCGATAATGCTTTCATCAGCCAGGGCGCGATAATCa                      >  1:1120757/1‑68 (MQ=255)
                    gccgACGAGGAACATCGCCAGCGTGCCGACAATCGATAATGCTTTCATCAGCCAGGGCGCGATAATCa                      >  1:1769374/1‑68 (MQ=255)
                    gccgACGAGGAACATCGCCAGCGTGCCGACAATCGATAATGCTTTCATCAGCCAGGGCGCGATAATCa                      >  1:1798676/1‑68 (MQ=255)
                    gccgACGAGGAACATCGCCAGCGTGCCGACAATCGATAATGCTTTCATCAGCCAGGGCGCGATAATCa                      >  1:1834991/1‑68 (MQ=255)
                    gccgACGAGGAACATCGCCAGCGTGCCGACAATCGATAATGCTTTCATCAGCCAGGGCGCGATAATCa                      >  1:2165706/1‑68 (MQ=255)
                    gccgACGAGGAACATCGCCAGCGTGCCGACAATCGATAATGCTTTCATCAGCCAGGGCGCGATAATCa                      >  1:2078602/1‑68 (MQ=255)
                    gccgACGAGGAACATCGCCAGCGTGCCGACAATCGATAATGCTTTCATCAGCCAGGGCGCGATAATCa                      >  1:2110692/1‑68 (MQ=255)
                         cgaGGAACATCGCCAGCGTGCCGACAATCGATAATGCTTTCATCAGCCAGGGCGCGAtt                          <  1:2510461/59‑2 (MQ=255)
                            ggAACATCGCCAGCGTGCCGACAATCGATAACGCTTTCATCAGCCAGGGCGCGATAATCAATAACCCtt             <  1:547639/69‑1 (MQ=255)
                            ggAACATCGCCAGCGTGCCGACAATCGATAACGCTTTCATCAGCCAGGGCGCGATAATCAATAACCCtt             <  1:1931361/69‑1 (MQ=255)
                            ggAACATCGCCAGCGTGCCGACAATCGATAACGCTTTCATCAGCCAGGGCGCGATAATCAATAACCCtt             <  1:1349146/69‑1 (MQ=255)
                            ggAACATCGCCAGCGTGCCGACAATCGATAACGCTTTCATCAGCCAGGGCGCGATAATCAATAACCCtt             <  1:1310326/69‑1 (MQ=255)
                                 aTCGCCAGCGTGCCGACAATCGATAATGCTTTCATCAGCCAGGGCGCGATAATCAATAACCCTTTACCt        <  1:1000321/69‑1 (MQ=255)
                                 aTCGCCAGCGTGCCGACAATCGATAATGCTTTCATCAGCCAGGGCGCGATAATCAATAACCCTTTACCt        <  1:1205291/69‑1 (MQ=255)
                                 aTCGCCAGCGTGCCGACAATCGATAATGCTTTCATCAGCCAGGGCGCGATAATCAATAACCCTTTACCt        <  1:997493/69‑1 (MQ=255)
                                 aTCGCCAGCGTGCCGACAATCGATAATGCTTTCATCAGCCAGGGCGCGATAATCAATAACCCTTTACCt        <  1:1322725/69‑1 (MQ=255)
                                 aTCGCCAGCGTGCCGACAATCGATAATGCTTTCATCAGCCAGGGCGCGATAATCAATAACCCTTTACCt        <  1:250159/69‑1 (MQ=255)
                                      cAGCGTGCCGACAATCGATAACGCTTTCATCAGCCAGGGCGCGATAATCAATAACCCTTTACCTAATGc   >  1:3097249/1‑69 (MQ=255)
                                      cAGCGTGCCGACAATCGATAACGCTTTCATCAGCCAGGGCGCGATAATCAATAACCCTTTACCTAATGc   >  1:453591/1‑69 (MQ=255)
                                      cAGCGTGCCGACAATCGATAACGCTTTCATCAGCCAGGGCGCGATAATCAATAACCCTTTACCTAATGc   >  1:1454053/1‑69 (MQ=255)
                                      cAGCGTGCCGACAATCGATAACGCTTTCATCAGCCAGGGCGCGATAATCAATAACCCTTTACCTAATGc   >  1:2680443/1‑69 (MQ=255)
                                      cAGCGTGCCGACAATCGATAACGCTTTCATCAGCCAGGGCGCGATAATCAATAACCCTTTACCTAATGc   >  1:593242/1‑69 (MQ=255)
                                      cAGCGTGCCGACAATCGATAACGCTTTCATCAGCCAGGGCGCGATAATCAATAACCCTTTACCTAATGc   >  1:1049927/1‑69 (MQ=255)
                                      cAGCGTGCCGACAATCGATAACGCTTTCATCAGCCAGGGCGCGATAATCAATAACCCTTTACCTAATGc   >  1:1862627/1‑69 (MQ=255)
                                       aGCGTGCCGACAATCGATAACGCTTTCATCAGCCAGGGCGCGATAATCAATAACCCTTTACCTAATGcc  >  1:2967056/1‑69 (MQ=255)
                                       aGCGTGCCGACAATCGATAACGCTTTCATCAGCCAGGGCGCGATAATCAATAACCCTTTACCTAATGcc  >  1:3274635/1‑69 (MQ=255)
                                                           |                                                
CCATGTACCACAATCCCACCGCCGACGAGGAACATCGCCAGCGTGCCGACAATCGATAACGCTTTCATCAGCCAGGGCGCGATAATCAATAACCCTTTACCTAATGCC  >  minE/1272854‑1272961

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