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
A1 F1 I1 R1 66 46.7 5280542 98.1% 5180211 47.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
MC JC NC_017635 3,614,356 Δ11 bp coding (1926‑1936/1941 nt) csrD ← RNase E specificity factor CsrD

Missing coverage evidence...
   seq id start end size ←reads reads→ gene description
* * ÷ NC_017635 3614356 3614366 11 40 [0] [0] 42 csrD RNase E specificity factor CsrD

New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_017635 = 36143550 (0.000)39 (0.780) 15/94 0.8 100% coding (1937/1941 nt) csrD RNase E specificity factor CsrD
?NC_017635 3614367 = 0 (0.000)coding (1925/1941 nt) csrD RNase E specificity factor CsrD

GATK/CNVnator alignment

BRESEQ :: bam2aln output
GACGCAGCGCGCGTTATTCTACGTGAAAACAGATTAAACGGCAGGTTAAACCGAGTATCTTTGTGAATATTTTTTCACGTTAGTATCAAGT  >  NC_017635/3614306‑3614396
                                                  |                                        
GACGCAGCGCGCGTTATTCTACGTGAAAACAGATTAAACGGCAGGTTAAAT                                          <  M01420:84:000000000‑ABVEH:1:1102:19084:2087/51‑1 (MQ=60)
GACGCAGCGCGCGTTATTCTACGTGAAAACAGATTAAACGGCAGGTTAAAT                                          >  M01420:84:000000000‑ABVEH:1:1110:8405:13288/1‑51 (MQ=60)
GACGCAGCGCGCGTTATTCTACGTGAAAACAGATTAAACGGCAGGTTAAAT                                          <  M01420:84:000000000‑ABVEH:1:2103:17355:18613/51‑1 (MQ=60)
            GTTATTCTACGTGAAAACAGATTAAACGGCAGGTTAAA‑‑‑‑‑‑‑‑‑‑‑TGTGAATATTTTT                   >  M01420:84:000000000‑ABVEH:1:2104:19901:8088/1‑51 (MQ=44)
                    ACGTGAAAACAGATTAAACGGCAGGTTAAA‑‑‑‑‑‑‑‑‑‑‑TGTGAATATTTTTTCACGTT            <  M01420:84:000000000‑ABVEH:1:2114:2171:16681/50‑1 (MQ=31)
                      GTGAAAACAGATTAAACGGCAGGTTAAA‑‑‑‑‑‑‑‑‑‑‑TGTGAATATTTTTTCACGTTAGT         <  M01420:84:000000000‑ABVEH:1:1105:21226:8466/51‑1 (MQ=33)
                      GTGAAAACAGATTAAACGGCAGGTTAAA‑‑‑‑‑‑‑‑‑‑‑TGTGAATATTTTTTCACGTTAGT         <  M01420:84:000000000‑ABVEH:1:1106:8054:4311/51‑1 (MQ=33)
                      GTGAAAACAGATTAAACGGCAGGTTAAA‑‑‑‑‑‑‑‑‑‑‑TGTGAATATTTTTTCACGTTAGT         <  M01420:84:000000000‑ABVEH:1:2114:8953:3679/51‑1 (MQ=33)
                        GAAAACAGATTAAACGGCAGGTTAAA‑‑‑‑‑‑‑‑‑‑‑TGTGAATATTTTTTCACGTTAGTA        <  M01420:84:000000000‑ABVEH:1:1112:9312:18097/50‑1 (MQ=31)
                         AAAACAGATTAAACGGCAGGTTAAA‑‑‑‑‑‑‑‑‑‑‑TGTGAATATTTTTTCACGTTAGTATC      >  M01420:84:000000000‑ABVEH:1:1101:11995:25930/1‑51 (MQ=33)
                         AAAACAGATTAAACGGCAGGTTAAA‑‑‑‑‑‑‑‑‑‑‑TGTGAATATTTTTTCACGTTAGTATC      <  M01420:84:000000000‑ABVEH:1:1105:21908:26587/51‑1 (MQ=33)
                         AAAACAGATTAAACGGCAGGTTAAA‑‑‑‑‑‑‑‑‑‑‑TGTGAATATTTTTTCACGTTAGTATC      <  M01420:84:000000000‑ABVEH:1:2106:7278:4354/51‑1 (MQ=33)
                             CAGATTAAACGGCAGGTTAAA‑‑‑‑‑‑‑‑‑‑‑TGTGAATATTTTTTCACGTTAGTATCAAGT  <  M01420:84:000000000‑ABVEH:1:1105:10420:7523/51‑1 (MQ=33)
                             CAGATTAAACGGCAGGTTAAA‑‑‑‑‑‑‑‑‑‑‑TGTGAATATTTTTTCACGTTAGTATCAAGT  <  M01420:84:000000000‑ABVEH:1:1111:14480:28463/51‑1 (MQ=33)
                             CAGATTAAACGGCAGGTTAAA‑‑‑‑‑‑‑‑‑‑‑TGTGAATATTTTTTCACGTTAGTATCAAGT  <  M01420:84:000000000‑ABVEH:1:2103:20508:26802/51‑1 (MQ=33)
                                                  |                                        
GACGCAGCGCGCGTTATTCTACGTGAAAACAGATTAAACGGCAGGTTAAACCGAGTATCTTTGTGAATATTTTTTCACGTTAGTATCAAGT  >  NC_017635/3614306‑3614396

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑