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
A19 F74 I1 R2	13	29.8	697290	91.1%	635231	133.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
JC	CP000730	62,818	+CAATTT	intergenic (+83/+228)	USA300HOU_0056 → / ← speG	hypothetical protein/diamine N‑acetyltransferase

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	CP000730	= 62817	0 (0.000)	14 (0.510) +TCAATT	13/250	1.2	100%	intergenic (+82/+229)	USA300HOU_0056/speG	hypothetical protein/diamine N‑acetyltransferase
*	?	CP000730	62818 =	0 (0.000)	14 (0.510) +TCAATT	13/250	1.2	100%	intergenic (+83/+228)	USA300HOU_0056/speG	hypothetical protein/diamine N‑acetyltransferase

AAGGCTTACTACAAAAAATGTTTGTGTAATTCTGATAACGTCCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  CP000730/62707‑62817

‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTACAGCGTCATCATTCATAAAATCCTCGTAGATTTTATCA  >  CP000730/62818‑62940

                                                                                                               ||||||

AAGGCTTACTACAAAAAATGTTTGTGTAATTCTGATAACGTCCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAG                                                                                                     >  1:99451/1‑141

                   GTTTGTGTAATTCTGATAACGTCCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGT                                                                                  <  1:77235/141‑1

                                                      TTGAAAATAGACAAAAATAAATTGAGAGCATCCATTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACC                                               >  2:119179/1‑141

                                                                  AAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTGAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTACAGCG                                   >  1:286965/1‑141

                                                                   AAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATTGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTACAGCGT                                  <  2:99451/141‑1

                                                                      ATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTACAGCGTCAT                               >  1:21318/1‑141

                                                                           TTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTACAGCGTCATCATTC                          >  2:191658/1‑141

                                                                           TTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAA                                                                                                      <  1:30261/65‑1

                                                                           TTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAA                                                                                                      >  2:30261/1‑65

                                                                             GAGAGCATCCCTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTACAGCGTCATCATTCAT                        >  1:11000/1‑141

                                                                                       CTTACCGCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTACAGCGTCATCATTCATAAAATCCTCG              <  2:115494/141‑1

                                                                                             GCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTA                                                 >  1:304959/1‑100

                                                                                             GCAAAGTGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTA                                                 <  2:304959/100‑1

                                                                                                   TGAAGGATGCTCTCAATTTATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTACAGCGTCATCATTCATAAAATCCTCGTAGATTTTATCA  >  1:77463/1‑141

                                                                                                               ||||||

AAGGCTTACTACAAAAAATGTTTGTGTAATTCTGATAACGTCCTATTATGTTAATTGAAAATAGACAAAAATAAATTGAGAGCATCCCTTACCGCAAAGTGAAGGATGCTC‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑  >  CP000730/62707‑62817

‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑‑TATTTTTGTTGAAATTAATATAAGCTTCATTCTGATAGATAGTCATTAATAATTGTTTGCAAATCGTTATTAAGTACCGTTGTTACAGCGTCATCATTCATAAAATCCTCGTAGATTTTATCA  >  CP000730/62818‑62940

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`
Reads not counted as support for junction
read_name Not counted due to insufficient overlap past the breakpoint.
read_name Not counted due to not crossing MOB target site duplication.

GATK/CNVnator alignment

N/A