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 1,620,888 A→G 52.1% S128S (AGT→AGC)  eutQ ← conserved hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,620,8880AG52.1% 0.9 / 44.9 55S128S (AGT→AGC) eutQconserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (23/3);  new base G (10/18);  total (34/21)
Fisher's exact test for biased strand distribution p-value = 8.04e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.89e-01

CAGTCAAGCCCACGCAATGCGGCTCTGCGCCGTCGAAACGACCAAACTTGACGCTACTGCCATCAATCACTTTGATGCCGCCTTTGCCGGTCACCGATTTGAAGC  >  minE/1620833‑1620937
                                                       |                                                 
cAGTCAAGCCCACGCAATGCGGCTCTGCGCCGTCGAAACGACCAAACTTGACGCTACTGCCatcaatca                                      >  1:444957/1‑69 (MQ=255)
         ccACGCAATGCGGCTCTGCGCCGTCGAAACGACCAAACTTGACGCTACTGCCATCAATCACTTTGATgc                             <  1:1287546/69‑1 (MQ=255)
         ccACGCAATGCGGCTCTGCGCCGTCGAAACGACCAAACTTGACGCTACTGCCATCAATCACTTTGATgc                             <  1:302631/69‑1 (MQ=255)
             gCAATGCGGCTCTGCGCCGTCGAAACGACCAAACTTGACGCTACTGCCATCAATCACTTTGATgccgcc                         <  1:1715299/69‑1 (MQ=255)
                  gCGGTTGTGCGCCGTCGAAACGACCAAACTTGACGCTGCTGCCATCAATAACTTTGATGCCGCCTTTGc                    <  1:2991575/69‑1 (MQ=255)
                  gCGGTTGTGCGCCGTCGAAACGACCAAACTTGACGCTGCTGCCATCAATAACTTTGATGCCGCCTTTGc                    <  1:2393324/69‑1 (MQ=255)
                  gCGGTTGTGCGCCGTCGAAACGACCAAACTTGACGCTGCTGCCATCAATAACTTTGATGCCGCCTTTGc                    <  1:3293319/69‑1 (MQ=255)
                  gCGGTTGTGCGCCGTCGAAACGACCAAACTTGACGCTGCTGCCATCAATAACTTTGATGCCGCCTTTGc                    <  1:3397466/69‑1 (MQ=255)
                  gCGGTTGTGCGCCGTCGAAACGACCAAACTTGACGCTGCTGCCATCAATAACTTTGATGCCGCCTTTGc                    <  1:344602/69‑1 (MQ=255)
                  gCGGTTGTGCGCCGTCGAAACGACCAAACTTGACGCTGCTGCCATCAATAACTTTGATGCCGCCTTTGc                    <  1:2154487/69‑1 (MQ=255)
                  gCGGTTGTGCGCCGTCGAAACGACCAAACTTGACGCTGCTGCCATCAATAACTTTGATGCCGCCTTTGc                    <  1:2088529/69‑1 (MQ=255)
                  gCGGTTGTGCGCCGTCGAAACGACCAAACTTGACGCTGCTGCCATCAATAACTTTGATGCCGCCTTTGc                    <  1:2612399/69‑1 (MQ=255)
                  gCGGTTGTGCGCCGTCGAAACGACCAAACTTGACGCTGCTGCCATCAATAACTTTGATGCCGCCTTTGc                    <  1:705601/69‑1 (MQ=255)
                  gCGGTTGTGCGCCGTCGAAACGACCAAACTTGACGCTGCTGCCATCAATAACTTTGATGCCGCCTTTGc                    <  1:789157/69‑1 (MQ=255)
                  gCGGTTGTGCGCCGTCGAAACGACCAAACTTGACGCTGCTGCCATCAATAACTTTGATGCCGCCTTTGc                    <  1:160381/69‑1 (MQ=255)
                  gCGGTTGTGCGCCGTCGAAACGACCAAACTTGACGCTGCTGCCATCAATAACTTTGATGCCGCCTTTGc                    <  1:1543700/69‑1 (MQ=255)
                  gCGGTTGTGCGCCGTCGAAACGACCAAACTTGACGCTGCTGCCATCAATAACTTTGATGCCGCCTTTGc                    <  1:1535369/69‑1 (MQ=255)
                  gCGGTTGTGCGCCGTCGAAACGACCAAACTTGACGCTGCTGCCATCAATAACTTTGATGCCGCCTTTGc                    <  1:845436/69‑1 (MQ=255)
                  gCGGTTGTGCGCCGTCGAAACGACCAAACTTGACGCTGCTGCCATCAATAACTTTGATGCCGCCTTTGc                    <  1:144704/69‑1 (MQ=255)
                  gCGGCTCTGCGCCGTCGAAACGACCAAACTTGACGCTACTGCCATCAATCACTTTGATGCCGCCTTTGc                    >  1:1844988/1‑69 (MQ=255)
                  gCGGCTCTGCGCCGTCGAAACGACCAAACTTGACGCTACTGCCATCAATCACTTTGATGCCGCCTTTGc                    >  1:1874625/1‑69 (MQ=255)
                  gCGGCTCTGCGCCGTCGAAACGACCAAACTTGACGCTACTGCCATCAATCACTTTGATGCCGCCTTTGc                    >  1:492798/1‑69 (MQ=255)
                  gCGGCTCTGCGCCGTCGAAACGACCAAACTTGACGCTACTGCCATCAATCACTTTGATGCCGCCTTTGc                    >  1:2261177/1‑69 (MQ=255)
                  gCGGCTCTGCGCCGTCGAAACGACCAAACTTGACGCTACTGCCATCAATCACTTTGATGCCGCCTTTGc                    >  1:1466429/1‑69 (MQ=255)
                  gCGGCTCTGCGCCGTCGAAACGACCAAACTTGACGCTACTGCCATCAATCACTTTGATGCCGCCTTTGc                    >  1:861215/1‑69 (MQ=255)
                  gCGGCTCTGCGCCGTCGAAACGACCAAACTTGACGCTACTGCCATCAATCACTTTGATGCCGCCTTTGc                    >  1:1294986/1‑69 (MQ=255)
                  gCGGCTCTGCGCCGTCGAAACGACCAAACTTGACGCTACTGCCATCAATCACTTTGATGCCGCCTTTGc                    >  1:2402135/1‑69 (MQ=255)
                  gCGGCTCTGCGCAGTCGAAACGACCAAACTTGACGCTACTGCCATCAATCACTTTGATGCCGCCTTTGc                    >  1:689561/1‑69 (MQ=255)
                                  gAAACGACCAAACTTGACGCTTCTGCCATCAATCACTTTGATGCCGCCTTTGCCGGTCACCGATTTGaa    >  1:3022885/1‑69 (MQ=255)
                                  gAAACGACCAAACTTGACGCTACTGCCATCAATCACTTTGATGCCGCCt                        >  1:2456102/1‑49 (MQ=255)
                                  gAAACGACCAAACTTGACGCTACTGCCATCAATCACTTTGATGCCGCCTTTGCCGGTCACCGATTTGaa    >  1:509079/1‑69 (MQ=255)
                                  gAAACGACCAAACTTGACGCTACTGCCATCAATCACTTTGATGCCGCCTTTGCCGGTCACCGATTTGaa    >  1:907879/1‑69 (MQ=255)
                                  gAAACGACCAAACTTGACGCTACTGCCATCAATCACTTTGATGCCGCCTTTGCCGGTCACCGATTTGaa    >  1:1013994/1‑69 (MQ=255)
                                  gAAACGACCAAACTTGACGCTACTGCCATCAATCACTTTGATGCCGCCTTTGCCGGTCACCGATTTGaa    >  1:290462/1‑69 (MQ=255)
                                  gAAACGACCAAACTTGACGCTACTGCCATCAATCACTTTGATGCCGCCTTTGCCGGTCACCGATTTGaa    >  1:2514313/1‑69 (MQ=255)
                                  gAAACGACCAAACTTGACGCTACTGCCATCAATCACTTTGATGCCGCCTTTGCCGGTCACCGATTTGaa    >  1:29260/1‑69 (MQ=255)
                                  gAAACGACCAAACTTGACGCTACTGCCATCAATCACTTTGATGCCGCCTTTGCCGGTCACCGATTTGaa    >  1:134466/1‑69 (MQ=255)
                                  gAAACGACCAAACTTGACGCTACTGCCATCAATCACTTTGATGCCGCCTTTGCCGGTCACCGATTTGaa    >  1:1519100/1‑69 (MQ=255)
                                  gAAACGACCAAACTTGACGCTACTGCCATCAATCACTTTGATGCCGCCTTTGCCGGTCACCGATTTGaa    >  1:198648/1‑69 (MQ=255)
                                  gAAACGACCAAACTTGACGCTACTGCCATCAATCACTTTGATGCCGCCTTTGCCGGTCACCGATTTGa     >  1:1077956/1‑68 (MQ=255)
                                  gAAACGACCAAACTTGACGCTACTGCCATCAATCACTTTGATGCCGCCTTTGCCGGTCACCGATTTGa     >  1:2489715/1‑68 (MQ=255)
                                  gAAACGACCAAACTTGACGCTACTGCCATCAATCACTTTGATCCCGCCTTTGCCGGTCACCGATTTGa     >  1:1856517/1‑68 (MQ=255)
                                           aaaCTTGACGCTGCTGCCATCAATAACTTTGATGCCGCCTTTGc                    <  1:3247464/44‑1 (MQ=38)
                                            aaCTTGACGCTGCTGCCATCAATAATTTTGATGCCGCCTTTGCCGGTCACCGATTTAAAGc  >  1:32838/1‑61 (MQ=255)
                                            aaCTTGACGCTGCTGCCATCAATAACTTTGATGCCGCCTTTGCCGGTCACCGATTTAAAg   >  1:2285500/1‑60 (MQ=255)
                                            aaCTTGACGCTGCTGCCATCAATAACTTTGATGCCGCCTTTGCCGGTCACCGATTTAAAGc  >  1:2369835/1‑61 (MQ=255)
                                            aaCTTGACGCTGCTGCCATCAATAACTTTGATGCCGCCTTTGCCGGTCACCGATTTAAAGc  >  1:2281609/1‑61 (MQ=255)
                                            aaCTTGACGCTGCTGCCATCAATAACTTTGATGCCGCCTTTGCCGGTCACCGATTTAAAGc  >  1:2103939/1‑61 (MQ=255)
                                            aaCTTGACGCTGCTGCCATCAATAACTTTGATGCCGCCTTTGCCGGTCACCGATTTAAAGc  >  1:2028218/1‑61 (MQ=255)
                                            aaCTTGACGCTGCTGCCATCAATAACTTTGATGCCGCCTTTGCCGGTCACCGATTTAAAGc  >  1:3215100/1‑61 (MQ=255)
                                            aaCTTGACGCTGCTGCCATCAATAACTTTGATGCCGCCTTTGCCGGTCACCGATTTAAAGc  >  1:839475/1‑61 (MQ=255)
                                            aaCTTGACGCTGCTGCCATCAATAACTTTGATGCCGCCTTTGCCGGTCACCGATTTAAAGc  >  1:3193420/1‑61 (MQ=255)
                                            aaCTTGACGCTGATGCCATCAATAACTTTGATGCCGCCTTTGCCGGTCACCGATTTAAAGc  >  1:2288352/1‑61 (MQ=255)
                                               ttGACGCTGCTGCCATCAATAACTTTGTTGCCGCCTTTGc                    <  1:3029402/40‑1 (MQ=37)
                                                  aCGCTGCTGCCATCAATAACTTTGATGCCGCCTTTGc                    <  1:183039/37‑1 (MQ=38)
                                                       |                                                 
CAGTCAAGCCCACGCAATGCGGCTCTGCGCCGTCGAAACGACCAAACTTGACGCTACTGCCATCAATCACTTTGATGCCGCCTTTGCCGGTCACCGATTTGAAGC  >  minE/1620833‑1620937

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