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
A30 F999 I0 R1	5	5.1	414173	44.8%	185549	128.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,188,282	G→A	R978H (CGT→CAT)	rpoC →	RNA polymerase subunit beta'

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,188,282	0	G	A	100.0%	14.0 / NA	9	R978H (CGT→CAT)	rpoC	RNA polymerase subunit beta'
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (2/7); total (2/7)

CGGCTGCTGAATCCAGCATCCAAGTGAAAAACAAAGGTAGCATCAAGCTCAGCAACGTGAAGTCGGTTGTGAACTCCAGCGGTAAACTGGTTATCACTTCCCGTAATACTGAACTGAAACTGATCGACGAATTCGGTCGTACTAAAGAAAGCTACAAAGTACCTTACGGTGCGGTACTGGCGAAAGGCGATGGCGAACAGGTTGCTGGCGGCGAAA  >  NC_000913/4188180‑4188395

cGGCTGCTGAATCCAGCATCCAAGTGAAAAACAAAGGTAGCATCAAGCCCAGCAACGTGAAGTCGGTTTTGAACTCCAGCGGTAAACTGGTTTTAACTTCCCATAAACCTAACCTGAAACTGGTcacca                                                                                         >  1:159323/1‑125 (MQ=255)

    tgctgAATCCAGCATCCAAGTGAAAAACAAAGGTAGCATCAAGCTCAGCAACGTGAAGTCGGTTGTGAACTCTAGCGGTAAACTGGTTATCACTTCCCATAATACTGAACTGAAACTGATCGACGAAtt                                                                                     <  1:175326/129‑1 (MQ=255)

     ctcgAAACCCGCATCCAAGGGAAAAACAAAGGTAGAATCAAGCCCAGCAACGGTAAGTCGGTTGTGAACTCCAGCGGTAAACTGGTTATCACTTCCCATAATACTGAACTGAAACTGATCGACGAATTc                                                                                    <  1:167842/126‑1 (MQ=255)

                 aTCCAAGTGAAAAACAAAGGTAGCATCAAGCTCAGCAACGTGAAGTCGGTTGTGAACTCCAGCGGTAAACTGGTTATCACTTCCCATAATACTGAACTGAAACGGAACGACGAATTCGGTGGTACaaa                                                                         >  1:184720/1‑128 (MQ=255)

                       aggAAAAACCAAGGGAGACTCAAGGCCAGGAACGTGAAGTCGGTTGTGAACTCCCGCGGTAAATTGGGTAACACTTCCCATAATACTGAACTGAAACTGATCGACGAATTCGGTCGTACTAAAGAAAGc                                                                  <  1:362317/127‑1 (MQ=255)

                                   ggTCGCAACAAGCTCAGAAACGTGAAGTTGGTTGTGAACTCAAGCGGTAAACTGGTTATCACTTCCCATAATACTGAACTGAAACTGATCGACGAATTCGGTCGTACTAAAGAAAGCTACAAAGTACCt                                                      <  1:155318/129‑1 (MQ=255)

                                        aaaaaaGCCCAGCACCGGGAGGTGGGTTGT‑AACCCCAGAGGTAAACTGGTTATCCCTTCCCATAATACTGAACTGAAACTGATCGACGAATTCGGTCGTACTAAAGAAAGCTACAAAGTACCTTACGGt                                                <  1:76953/125‑1 (MQ=255)

                                                                        aCTCCCGGGGGAAACTGGTTAACACCTCCCATAATTATGAACTGAATCCGATCGACGAATTCGGTCGTACTAAAGAAAGCTACAAAGTACCTTACGGTGCGGTACTGGCGAAAGGCGATGGCGAACAgg                 <  1:183513/129‑1 (MQ=255)

                                                                                      ttGGTTATCA‑TTCCCAAAAAACCGAACCTGAACTGGTCGCCAAATTCGGTCGTACGAAAGAAAGCTACAAAGTACCTTACGGTGCGGTACTGGCGAAAGGCGATGGCGAACAGGTTGCTGGCGGCGaaa  <  1:326468/128‑1 (MQ=255)

CGGCTGCTGAATCCAGCATCCAAGTGAAAAACAAAGGTAGCATCAAGCTCAGCAACGTGAAGTCGGTTGTGAACTCCAGCGGTAAACTGGTTATCACTTCCCGTAATACTGAACTGAAACTGATCGACGAATTCGGTCGTACTAAAGAAAGCTACAAAGTACCTTACGGTGCGGTACTGGCGAAAGGCGATGGCGAACAGGTTGCTGGCGGCGAAA  >  NC_000913/4188180‑4188395

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 8 ≤` `ATCG/ATCG` `< 9 ≤` `ATCG/ATCG` `< 23 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A