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
A3 F48 I1 R1	58	71.3	3054194	98.3%	3002272	146.3

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_002947_CJ‑RC	1,499,498	1 bp→CG	intergenic (+75/‑89)	trpS → / → zapE	tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947_CJ‑RC	1,499,497	1	.	C	81.8%	26.2 / 0.8	11	intergenic (+74/‑90)	trpS/zapE	tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein
Reads supporting (aligned to +/- strand): ref base . (0/2); new base C (8/1); total (8/3)
Fisher's exact test for biased strand distribution p-value = 5.45e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
*	NC_002947_CJ‑RC	1,499,498	0	T	G	100.0%	31.3 / NA	11	intergenic (+75/‑89)	trpS/zapE	tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein
Reads supporting (aligned to +/- strand): ref base T (0/0); new base G (8/3); total (8/3)

AGCAGGACTGAGGCTGCCAAACGGTGGGAGCGGGCGTGCCCGCGAAACAGGCGCCGCGGTGCATGGCCAC‑GGCTTTGCCGGT‑GTT‑TCG‑GG‑CA‑CG‑CCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTATCAAGCAGATCTGAAACGTCCCGACTTCTTCCATGAC  >  NC_002947_CJ‑RC/1499413‑1499643

||

agccgGACTGCGGCGGCCACCGGGGGGGCGGGGGCGTCCCCCCTAAACCGGCGCGGCGGTGC‑TGGCCCCGGGCTTTGCCGGTGGGC‑GCG‑GG‑CA‑CGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGcc                                                                                      <  6:337651/149‑1 (MQ=255)

                               gggCGCGCCCGCCAACCTGCCCCCG‑GGTGCCTGGCCAC‑GGCGTGGCCGGG‑GGT‑GCGCGGCCACCC‑CCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTAACGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGa                                                       <  6:259407/149‑1 (MQ=255)

                                      cccGCGAAACAGGCGCCGCGGTGCATGGCACC‑GGCTTTGCCGGA‑GTTCGCG‑GG‑CA‑CGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGGTTTTTGTTGCCTCGCTAACGAATCATGACTCCCt                                                 >  8:101656/1‑148 (MQ=25)

                                       ccGCGAAACAGGCGCCGCGGTGCATGGCACC‑GGCTTTGCCGGT‑GTTCGCG‑GG‑CA‑CGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCt                                                 >  4:115949/1‑147 (MQ=37)

                                       ccGCGAAACAGGCGCCGCGGTGCATGGCACC‑GGCTTTGCCGGT‑GTTCGCG‑GG‑CA‑CGCCCGCTCCCACAGACTGATAGCCATAAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCACGCTAACGAATCATGACTccca                                                 >  8:265790/1‑146 (MQ=25)

                                         gcgAAACAGGCGCCGCGGTGCATGGCACC‑GGCTTTGCCGGT‑GTTCGCG‑GG‑CA‑CGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAg                                              >  5:153282/1‑148 (MQ=37)

                                         gcgAAACAGGCGCCGCGGTGCATGACACC‑GGCTTTGCCGGT‑GTTCGCG‑GG‑CA‑CGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAg                                              >  5:44983/1‑148 (MQ=37)

                                                   cgccgcGGTGCATGGCACC‑GGCTTTGCCGGT‑GTTCGCG‑GG‑CA‑CGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTATCaa                                   <  6:153282/149‑1 (MQ=37)

                                                      cgcgGTGCATGGCACC‑GGCTTTGCCGGT‑GTTCGCG‑GG‑CA‑CGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTATCAAg                                  >  1:367499/1‑147 (MQ=37)

                                                                     c‑GGCTTTGCCGGT‑GTTCGCG‑GG‑CC‑CGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTATCAAGCAGATCTGAAACGTccc                 >  3:332528/1‑149 (MQ=39)

                                                                          tttGCCGGT‑GTTCGCG‑GG‑CA‑CGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTATCAAGCAGATCTGAAACGTCCCGAct             >  2:53492/1‑149 (MQ=39)

                                                                                      tcgcG‑GG‑CA‑CGCCCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTATCAAGCAGATCTGAAACGTCCCGACTTCTTCCATGAc  >  4:50787/4‑149 (MQ=255)

||

AGCAGGACTGAGGCTGCCAAACGGTGGGAGCGGGCGTGCCCGCGAAACAGGCGCCGCGGTGCATGGCCAC‑GGCTTTGCCGGT‑GTT‑TCG‑GG‑CA‑CG‑CCGCTCCCACAGACTGATTGCCATTAAGCGGGCCTATCGCTACAGTGACGGCCCGTTTTTTGTTGCCTCGCTAACGAATCATGACTCCCTTAGAACGCTATCAAGCAGATCTGAAACGTCCCGACTTCTTCCATGAC  >  NC_002947_CJ‑RC/1499413‑1499643

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 15 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A