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 1,948,611 G→A 31.5% D69D (GAC→GAT)  gcvH ← glycine cleavage complex lipoylprotein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,948,6110GA31.5% 49.1 / 26.0 57D69D (GAC→GAT) gcvHglycine cleavage complex lipoylprotein
Reads supporting (aligned to +/- strand):  ref base G (18/21);  new base A (7/11);  total (25/32)
Fisher's exact test for biased strand distribution p-value = 7.75e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.84e-01

GCCACGATTTCACCGCTTACTGGCGCATAAATGTCTGACGCCGCTTTTACCGATTCGGCAACCGCGCAGTCATCGCCCGCGCTAACCGTTGCGCCCAC  >  minE/1948579‑1948676
                                |                                                                 
gCCACGATTTCACCGCTTACTGGCGCATACATGTCTGACGCCGCTTTTACCGATTCGGCAACCGCGCa                                <  1:2829551/68‑1 (MQ=255)
gCCACGATTTCACCGCTTACTGGCGCATAAATGTCTGACGCCGCTTTTACCGATTCGGCAACCGCGCa                                >  1:1159130/1‑68 (MQ=255)
gCCACGATTTCACCGCTTACTGGCGCATAAATGTCTGACGCCGCTTTTACCGATTCGGCAACCGCGCa                                <  1:2578/68‑1 (MQ=255)
gCCACGATTTCACCGCTTACTGGCGCATAAATGTCTGACGCCGCTTTTACCGATTCGGCAACCGCGCa                                <  1:932827/68‑1 (MQ=255)
gCCACGATTTCACCGCTTACTGGCGCATAAATGTCTGACGCCGCTTTTACCGATTCGGCAACCGCGCa                                <  1:824274/68‑1 (MQ=255)
gCCACGATTTCACCGCTTACTGGCGCATAAATGTCTGACGCCGCTTTTACCGATTCGGCAACCGCGCa                                >  1:3125329/1‑68 (MQ=255)
gCCACGATTTCACCGCTTACTGGCGCATAAATGTCTGACGCCGCTTTTACCGATTCGGCAACCGCGCa                                >  1:2327120/1‑68 (MQ=255)
gCCACGATTTCACCGCTTACTGGCGCATAAATGTCTGACGCCGCTTTTACCGATTCGGCAACCGCGCa                                >  1:2200304/1‑68 (MQ=255)
gCCACGATTTCACCGCTTACTGGCGCATAAATGTCTGACGCCGCTTTTACCGATTCGGCAACCGCGCa                                <  1:1474334/68‑1 (MQ=255)
gCCACGATTTCACCGCTTACTGGCGCATAAATGTCTGACGCCGCTTTTACCGATTCGGCAACCGCGCa                                >  1:654164/1‑68 (MQ=255)
gCCACGATTTCACCGCTTACTGGCGCATAAATGTCTGACGCCGCTTTTACCGATTCGGCAACCGCGCa                                >  1:18174/1‑68 (MQ=255)
gCCACGATTTCACCGCTTACTGGCGCATAAATATCTGACGCCGCTTTTACCGATTCGGCAACCGCGCAg                               <  1:278316/69‑1 (MQ=255)
gCCACGATTTCACCGCTTACTGGCGCATAAATATCTGACGCCGCTTTTACCGATTCGGCAACCGCGCAg                               <  1:297959/69‑1 (MQ=255)
gCCACGATTTCACCGCTTACTGGCGCATAAATATCTGACGCCGCTTTTACCGATTCGGCAACCGCGCAg                               <  1:3089806/69‑1 (MQ=255)
gCCACGATTTCACCGCTTACTGGCGCATAAATATCTGACGCCGCTTTTACCGATTCGGCAACCGCGCAg                               <  1:3349155/69‑1 (MQ=255)
gCCACGATTTCACCGCTTACTGGCGCATAAATATCTGACGCCGCTTTTACCGATTCGGCAACCGCGCAg                               <  1:370868/69‑1 (MQ=255)
gCCACGATTTCACCGCTTACTGGCGCATAAATATCTGACGCCGCTTTTACCGATTCGGCAACCGCGCAg                               <  1:676750/69‑1 (MQ=255)
gCCACGATTTCACCGCTTACTGGCGCATAAATATCTGACGCCGCTTTTACCGATTCGGCAACCGCGCAg                               <  1:1580518/69‑1 (MQ=255)
gCCACGATTTCACCGCTTACTGGCGCATAAATATCTGACGCCGCTTTTACCGATTCGGCAACCGCGCAg                               <  1:1462280/69‑1 (MQ=255)
gCCACGATTTCACCGCTTACTGGCGCATAAATATCTGACGCCGCTTTTACCGATTCGGCAACCGCGCAg                               <  1:944066/69‑1 (MQ=255)
gCCACGATTTCACCGCTTACTGGCGCATAAATATCTGACGCCGCTTTTACCGATTCGGCAACCGCGCAg                               <  1:117540/69‑1 (MQ=255)
 ccACGATTTCACCGCTTACTGGCGCATAAATATCTGACGCCGCTTTTACCGATTCGGCAACCGCGCAg                               <  1:521399/68‑1 (MQ=255)
  cACGATTTCACCGCTTACTGGCGCATAAATGTCTGACGCCGCTTTTACCGATTCGGCAACCGCGCAGTc                             <  1:1882465/69‑1 (MQ=255)
  cACGATTTCACCGCTTACTGGCGCATAAATGTCTGACGCCGCTTTTACCGATTCGGCAACCGCGCAGTc                             <  1:1970286/69‑1 (MQ=255)
           aCCGCTTACTGGCGCATAAATATCTGACGCCGCTTTTACCGATTCGGCAACCGCGCAGTCATCGCCcgc                    >  1:1614024/1‑69 (MQ=255)
           aCCGCTTACTGGCGCATAAATATCTGACGCCGCTTTTACCGATTCGGCAACCGCGCAGTCATCGCCcgc                    >  1:2759852/1‑69 (MQ=255)
           aCCGCTTACTGGCGCATAAATATCTGACGCCGCTTTTACCGATTCGGCAACCGCGCAGTCATCGCCcgc                    >  1:2724733/1‑69 (MQ=255)
           aCCGCTTACTGGCGCATAAATATCTGACGCCGCTTTTACCGATTCGGCAACCGCGCAGTCATCGCCcgc                    >  1:1211861/1‑69 (MQ=255)
           aCCGCTTACTGGCGCATAAATATCTGACGCCGCTTTTACCGATTCGGCAACCGCGCAGTCATCGCCcgc                    >  1:843309/1‑69 (MQ=255)
           aCCGCTTACTGGCGCATAAATATCTGACGCCGCTTTTACCGATTCGGCAACCGCGCAGTCATCGCCcgc                    >  1:1344162/1‑69 (MQ=255)
           aCCGCTTACTGGCGCATAAATATCTGACGCCGCTTTTACCGATTCGGCAACCGCGCAGTCATCGCCcgc                    >  1:1422981/1‑69 (MQ=255)
                 tACTGGCGCATAAATGTCTGACGCCGCTTTTACCGATTCGGCAACCGCGCAGTCATCGCCCGGGCTAAc              <  1:6790/69‑1 (MQ=255)
                 tACTGGCGCATAAATGTCTGACGCCGCTTTTACCGATTCGGCAACCGCGCAGTCATCGCCCGCGCTAAc              <  1:744901/69‑1 (MQ=255)
                 tACTGGCGCATAAATGTCTGACGCCGCTTTTACCGATTCGGCAACCGCGCAGTCATCGCCCGCGCTAAc              <  1:380969/69‑1 (MQ=255)
                 tACTGGCGCATAAATGTCTGACGCCGCTTTTACCGATTCGGCAACCGCGCAGTCATCGCCCGCGCTAAc              <  1:2429124/69‑1 (MQ=255)
                 tACTGGCGCATAAATGTCTGACGCCGCTTTTACCGATTCGGCAACCGCGCAGTCATCGCCCGCGCTAAc              <  1:2531511/69‑1 (MQ=255)
                 tACTGGCGCATAAATGTCTGACGCCGCTTTTACCGATTCGGCAACCGCGCAGTCATCGCCCGCGCTAAc              <  1:1001304/69‑1 (MQ=255)
                 tACTGGCGCATAAATGTCTGACGCCGCTTTTACCGATTCGGCAACCGCGCAGTCATCGCCCGCGCTAAc              <  1:2365947/69‑1 (MQ=255)
                 tACTGGCGCATAAATGTCTGACGCCGCTTTTACCGATTCGGCAACCGCGCAGTCATCGCCCGCGCTAAc              <  1:1249405/69‑1 (MQ=255)
                 tACTGGCGCATAAATGTCTGACGCCGCTTTTACCGATTCGGCAACCGCGCAGTCATCGCCCGCGCTAAc              <  1:2238009/69‑1 (MQ=255)
                 tACTGGCGCATAAATGTCTGACGCCGCTTTTACCGATTCGGCAACCGCGCAGTCATCGCCCGCGCTAAc              <  1:2195331/69‑1 (MQ=255)
                 tACTGGCGCATAAATGTCTGACGCCGCTTTTACCGATTCGGCAACCGCGCAGTCATCGCCCGCGCTAAc              <  1:2183012/69‑1 (MQ=255)
                 tACTGGCGCATAAATGTCTGACGCCGCTTTTACCGATTCGGCAACCGCGCAGTCATCGCCCGCGCTAAc              <  1:1265430/69‑1 (MQ=255)
                 tACTGGCGCATAAATGTCTGACGCCGCTTTTACCGATTCGGCAACCGCGCAGTCATCGCCCGCGCTAAc              <  1:2651387/69‑1 (MQ=255)
                 tACTGGCGCATAAATGTCTGACGCCGCTTTTACCGATTCGGCAACCGCGCAGTCATCGCCCGCGCTAAc              <  1:1974756/69‑1 (MQ=255)
                             aaTGTCTGACGCCGCTTTTACCGATTCGGCAACCGCGCAGTCATCGCCCGCGCTAACCGTTGCGCCCAc  >  1:613881/1‑69 (MQ=255)
                             aaTGTCTGACGCCGCTTTTACCGATTCGGCAACCGCGCAGTCATCGCCCGCGCTAACCGTTGCGCCCAc  >  1:1116976/1‑69 (MQ=255)
                             aaTGTCTGACGCCGCTTTTACCGATTCGGCAACCGCGCAGTCATCGCCCGCGCTAACCGTTGCGCCCAc  >  1:1229050/1‑69 (MQ=255)
                             aaTGTCTGACGCCGCTTTTACCGATTCGGCAACCGCGCAGTCATCGCCCGCGCTAACCGTTGCGCCCAc  >  1:812405/1‑69 (MQ=255)
                             aaTGTCTGACGCCGCTTTTACCGATTCGGCAACCGCGCAGTCATCGCCCGCGCTAACCGTTGCGCCCAc  >  1:1317399/1‑69 (MQ=255)
                             aaTGTCTGACGCCGCTTTTACCGATTCGGCAACCGCGCAGTCATCGCCCGCGCTAACCGTTGCGCCCAc  >  1:715651/1‑69 (MQ=255)
                             aaTGTCTGACGCCGCTTTTACCGATTCGGCAACCGCGCAGTCATCGCCCGCGCTAACCGTTGCGCCCAc  >  1:1555574/1‑69 (MQ=255)
                             aaTGTCTGACGCCGCTTTTACCGATTCGGCAACCGCGCAGTCATCGCCCGCGCTAACCGTTGCGCCCAc  >  1:1736645/1‑69 (MQ=255)
                             aaTGTCTGACGCCGCTTTTACCGATTCGGCAACCGCGCAGTCATCGCCCGCGCTAACCGTTGCGCCCAc  >  1:2137532/1‑69 (MQ=255)
                             aaTGTCTGACGCCGCTTTTACCGATTCGGCAACCGCGCAGTCATCGCCCGCGCTAACCGTTGCGCCCAc  >  1:3182602/1‑69 (MQ=255)
                             aaTGTCTGACGCCGCTTTTACCGATTCGGCAACCGCGCAGTCATCGCCCGCGCTAACCGTTGCGCCCAc  >  1:3154804/1‑69 (MQ=255)
                             aaTGTCTGACGCCGCTTTTACCGATTCGGCAACCGCGCAGTCATCGCCCGCGCTAACCGTTGCGCCCAc  >  1:2916996/1‑69 (MQ=255)
                                |                                                                 
GCCACGATTTCACCGCTTACTGGCGCATAAATGTCTGACGCCGCTTTTACCGATTCGGCAACCGCGCAGTCATCGCCCGCGCTAACCGTTGCGCCCAC  >  minE/1948579‑1948676

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A