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 F5 I184 R1	278	29.6	1166432	97.3%	1134938	124.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	871,743	A→G	E318G (GAA→GGA)	dgcI →	GGDEF domain‑containing protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	871,743	0	A	G	100.0%	52.8 / NA	16	E318G (GAA→GGA)	dgcI	GGDEF domain‑containing protein
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (9/7); total (9/7)

ACTGGATGGCGGGCTTTTCTTTTCGGCTGCCGATGTCAAAAAACTCTACAGTATGTATAACTCGGCGTTCCTGGACGACCTGACCAAAGCAATGGGCAGAAAATCCTTTGACGAAGATTTAAAAGCGCTGCCGGAAAAAGGCGGTTATTTGTGCCTGTTTGACGTCGATAAATTCAAAAACATTAACGACACCTTCGGTCATTTGCTGGGCGATGAAGTGTTGATGAAAGTGGTGAAAATCCTTAAATCACAGATCCCGGTAGATAAAG  >  NZ_CP009273/871609‑871877

aCTGGATGGCGGGCTTTTCTTTTCGGCTGCCGATGTCAAAAAACTCTACAGTATGTATAACTCGGCGTTCCTGGACGACCTGACCAAAGCAATGGGCAGAAAATCCTTTGACGAAGATTTAAAAGCGCTGCCGGgaa                                                                                                                                      >  1:211899/1‑137 (MQ=255)

         cGGGCTTTTCTTTTCGGCTGCCGATGTCAAAAAACTCTACAGTATGTATAACTCGGCGTTCCTGGACGACCTGACCAAAGCAATGGGCAGAAAATCCTTTGACGAAGATTTAAAAGCGCTGCCGGGAAAAGGCGGTTAt                                                                                                                           >  2:162357/1‑139 (MQ=255)

                ttcttttcGGCTGCCGATGTCAAAAAACTCTACAGTATGTATAACTCGGCGTTCCTGGACGACCTGACCAAAGCAATGGGCAGAAAATCCTTTGACGAAGATTTAAAAGCGCTGCCGGGAAAAGGCGGTTATTTGTGc                                                                                                                     <  2:298747/138‑1 (MQ=255)

                ttcttttcGGCTGCCGATGTCAAAAAACTCTACAGTATGTATAACTCGGCGTTCCTGGACGACCTGACCAAAGCAATGGGCAGAAAATCCTTTGACGAAGATTTAAAAGCGCTGCCGGGAAAAGGCGGTTATTTGTGc                                                                                                                     <  1:566705/138‑1 (MQ=255)

                                                     tgtatAACTCGGCGTTCCTGGACGACCTGACCAAAGCAATGGGCAGAAAATCCTTTGACGAAGATTTAAAAGCGCTGCCGGGAAAAGGCgg                                                                                                                               >  2:446360/1‑91 (MQ=255)

                                                     tgtatAACTCGGCGTTCCTGGACGACCTGACCAAAGCAATGGGCAGAAAATCCTTTGACGAAGATTTAAAAGCGCTGCCGGGAAAAGGCgg                                                                                                                               <  1:446360/91‑1 (MQ=255)

                                                                 cGTTCCTGGACGACCTGACCAAAGCAATGGGCAGAAAATCCTTTGACGAAGATTTAAAAGCGCTGCCGGGAAAAGGCGGTTATTTGTGCCTGTTTGACGTCGATAAATTCAAAAACATTAACGACACCTTCGGTCAttt                                                                   >  2:56145/1‑139 (MQ=255)

                                                                                       aGCAATGGGCAGAAAATCCTTTGACGACGATTTAAAAGAGCTGCCGGGAAAAGGCGGTTATTTGTGCCTGTTTGACGTCGATAAATTCAAAAACATTAACGACACCTTCGGTCATTTGCTGGGCGATGGAGTGTtgat                                              >  2:203905/1‑138 (MQ=255)

                                                                                       aGCAATGGGCAGAAAATCCTTTGACGAAGATTTAAAAGCGCTGCCGGGAAAAGGCGGTTATTTGTGCCTGTTTGACGTCGATAAATTCAAAAACATTAACGACACCTTCGGTCATTTGCTGGGCGATGAAGTGTtgat                                              >  2:265518/1‑138 (MQ=255)

                                                                                            tGGGCAGAAAATCCTTTGACGAAGATTTAAAAGCGCTGCCGGGAAAAGGCGGTTATTTGTGCCTGTTTGACGTCGATa                                                                                                     >  1:346629/1‑78 (MQ=255)

                                                                                            tGGGCAGAAAATCCTTTGACGAAGATTTAAAAGCGCTGCCGGGAAAAGGCGGTTATTTGTGCCTGTTTGACGTCGATa                                                                                                     <  2:346629/78‑1 (MQ=255)

                                                                                                        ccTTTGACGAAGATTTAAAGGCGCTGCCGGGAAAAGGCGGTTATTTGTGCCTGTTTGACGTCGATAAATTCAAAAACATTAACGACACCTTCGGTCATTTGCTGGGCGATGaa                                                      >  2:221405/1‑113 (MQ=255)

                                                                                                        ccTTTGACGAAGATTTAAAGGCGCTGCCGGGAAAAGGCGGTTATTTGTGCCTGTTTGACGTCGATAAATTCAAAAACATTAACGACACCTTCGGTCATTTGCTGGGCGATGaa                                                      <  1:221405/113‑1 (MQ=255)

                                                                                                                              gcTGCCGGGAAAAGGCGGTTATTTGTGCCTGTTTGACGTCGATAAATTCAAAAACATTAACGACACCTTCGGTCATTTGCTGGGCGATg                                                        >  2:208030/1‑89 (MQ=255)

                                                                                                                              gcTGCCGGGAAAAGGCGGTTATTTGTGCCTGTTTGACGTCGATAAATTCAAAAACATTAACGACACCTTCGGTCATTTGCTGGGCGATg                                                        <  1:208030/89‑1 (MQ=255)

                                                                                                                               cTGCCGGGAAAAGGCGGTTATTTGTGCCTGTTTGACGTCGATAAATTCAAAAACATTAACGACACCTTCGGTCATTTGCTGGGCGATGAAGTGTTGATGAAAGTGGTGAAAATCCTTAAATCACAGATCCCGGTAGAt      >  2:482714/1‑138 (MQ=255)

                                                                                                                                  ccGGGAAAAGGCGGTTATTTGTGCCTGTTTGACGTCGATAAATTCAAAAACATTAACGACACCTTCGGTCATTTGCTGGGCGATGAAGTGTTGATGAAAGTGGTGAAAATCCTTAAATCACAGATCCCGGTAGATAAAg  <  1:265518/139‑1 (MQ=255)

ACTGGATGGCGGGCTTTTCTTTTCGGCTGCCGATGTCAAAAAACTCTACAGTATGTATAACTCGGCGTTCCTGGACGACCTGACCAAAGCAATGGGCAGAAAATCCTTTGACGAAGATTTAAAAGCGCTGCCGGAAAAAGGCGGTTATTTGTGCCTGTTTGACGTCGATAAATTCAAAAACATTAACGACACCTTCGGTCATTTGCTGGGCGATGAAGTGTTGATGAAAGTGGTGAAAATCCTTAAATCACAGATCCCGGTAGATAAAG  >  NZ_CP009273/871609‑871877

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

BRESEQ :: bam2aln output

TTTGAACGCGTACTGGATGGCGGGCTTTTCTTTTCGGCTGCCGATGTCAAAAAACTCTACAGTATGTATAACTCGGCGTTCCTGGACGACCTGACCAAAGCAATGGGCAGAAAATCCTTTGACGAAGATTTAAAAGCGCTGCCGGAAAAAGGCGGTTATTTGTGCCTGTTTGACGTCGATAAATTCAAAAACATTAACGACACCTTCGGTCATTTGCTGGGCGATGAAGTGTTGATGAAAGTGGTGAAAATCCTTAAATCACAGATCCCGGTAGATAAAGGTAAAGTCTAC  >  NZ_CP009273/871598‑871888

TTTGAACGCGTACTGGATGGCGGGCTTTTCTTTTCGGCTGCCGATGTCAAAAAACTCTACAGTATGTATAACTCGGCGTTCCTGGACGACCTGACCAAAGCAATGGGCAGAAAATCCTTTGACGAAGATTTAAAAGCGCTGCCGGGAAA                                                                                                                                                >  SRR3722139.214524/1‑149 (MQ=60)

                acggtctcgtgggctcggagatgtgtataagagacagACTCTACAGTATGTATAACTCGGCGTTCCTGGACGACCTGACCAAAGCAATGGGCAGAAAATCCTTTGACGAAGATTTAAAAGCGCTGCCGGGAAAAGGCGGTTATTTGTGCC                                                                                                                               <  SRR3722139.451596/113‑1 (MQ=60)

                          TTTCTTTTCGGCTGCCGATGTCAAAAAACTCTACAGTATGTATAACTCGGCGTTCCTGGACGACCTGACCAAAGCAATGGGCAGAAAATCCTTTGACGAAGATTTAAAAGCGCTGCCGGGAAAAGGCGGTTATTTGTGCCTGTTTGACGT                                                                                                                     <  SRR3722139.573205/150‑1 (MQ=60)

                                                                                      agtacggtctcgtgggctcggagatgtgtataagagacagGATTTAAAAGCGCTGCCGGGAAAAGGCGGTTATTTGTGCCTGTTTGACGTCGATAAATTCAAAAACATTAACGACACCTTCGGTCATTTGCTGGGCGATGAAGTGTTGATG                                                        <  SRR3722139.210621/111‑1 (MQ=60)

                                                                                         gtgtataagagacagGGGCAGAAAATCCTTTGACGAAGATTTAAAGGCGCTGCCGGGAAAAGGCGGTTATTTGTGCCTGTTTGACGTCGATAAATTCAAAAACATTAACGACACCTTCGGTCATTTGCTGGGCGATGAAGTGTTGATGAA                                                      <  SRR3722139.224123/135‑1 (MQ=60)

                                                                                            GACCAAAGCAATGGGCAGAAAATCCTTTGACGAAGATTTAAAAGCGCTGCCGGGAAAAGGCGGTTATTTGTGCCTGTTTGACGTCGATAAATTCAAAAACctgtctcttatacacatctccgagcccacgagaccgtactagatctcgtat                                                  >  SRR3722139.350825/1‑100 (MQ=60)

                                                                                                                                            GCCGGGAAAAGGCGGTTATTTGTGCCTGTTTGACGTCGATAAATTCAAAAACATTAACGACACCTTCGGTCATTTGCTGGGCGATGAAGTGTTGATGAAAGTGGTGAAAATCCTTAAATCACAGATCCCGGTAGATAAAGGTAAAGTCTAC  <  SRR3722139.268851/151‑1 (MQ=60)

TTTGAACGCGTACTGGATGGCGGGCTTTTCTTTTCGGCTGCCGATGTCAAAAAACTCTACAGTATGTATAACTCGGCGTTCCTGGACGACCTGACCAAAGCAATGGGCAGAAAATCCTTTGACGAAGATTTAAAAGCGCTGCCGGAAAAAGGCGGTTATTTGTGCCTGTTTGACGTCGATAAATTCAAAAACATTAACGACACCTTCGGTCATTTGCTGGGCGATGAAGTGTTGATGAAAGTGGTGAAAATCCTTAAATCACAGATCCCGGTAGATAAAGGTAAAGTCTAC  >  NZ_CP009273/871598‑871888

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`