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
A35 F30 I1 R1	29	21.9	747794	99.4%	743307	139.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,376,989	Δ1 bp	coding (604/759 nt)	menH ←	2‑succinyl‑6‑hydroxy‑2, 4‑cyclohexadiene‑1‑carboxylate synthase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,376,986	0	A	.	100.0%	54.8 / NA	14	coding (607/759 nt)	menH	2‑succinyl‑6‑hydroxy‑2, 4‑cyclohexadiene‑1‑carboxylate synthase
Reads supporting (aligned to +/- strand): ref base A (0/0); new base . (6/8); total (6/8)

TACGCCAGCGGGATTTTCCCGATGCGCGTTATGTCCGGCGCGAGGAATGACATGGCAGTCGGCAGCCAGTTCCGCCGCCAGGGCGCGGAATTTGCTGTCACGTTCACCACATAAATAATAAAACGCAAATGTGCGGGCGCTAAGGTTAGCACGTAAATCAGGCTGGACGGCGAGAGAAGTCGCCTCCAGCATGGCGGCAAGCGTTGCGCCATTATTGTTGCTGCGCAGCGCCACCAGCTCCCGGCGTTGATCGTC  >  NC_000913/2376867‑2377121

tACGCCAGCGGGATTTTCCCGATGCGCGTTATGTCCGGCGCGAGGAATGACATGGCAGTCGGCAGCCAGTTCCGCCGCCAGGGCGCGGAATTTGCTGTCACGTTCACCACATAAATAAT‑AAACGCAAATGTGCGGGCGCt                                                                                                                    <  2:86863/140‑1 (MQ=255)

                                          aGGAATGACATGGCAGTCGGCAGCCAGTTCCGCCGCCAGGGCGCGGAATTTGCTGTCACGTTCACCACATAAATAAT‑AAACGCAAATGTGCGGGCGCTAAGGTTAGCACGTAAATCAGGCTGGACGGCGAGAGAAGTCGc                                                                          >  1:104561/1‑140 (MQ=255)

                                           ggAATGACATGGCAGTCGGCAGCCAGTTCCGCCGCCAGGGCGCGGAATTTGCTGTCACGTTCACCACATAAATAAT‑AAACGCAAATGTGCGGGCGCTAAGGTTAGCACGTAAATCAGGCTGGACGGCGAGAGAAGTCGcc                                                                         <  1:200043/140‑1 (MQ=255)

                                                       cAGTCGGCAGCCAGTTCCGCCGCCAGGGCGCGGAATTTGCTGTCACGTTCACCACATAAATAAT‑AAACGCAAATGTGCGGGCGCTAAGGTTAGCACGTAAATCAGGCTGGACGGCGAGAGAAGTCGCCTCCAGCATggcg                                                             >  2:285618/1‑140 (MQ=255)

                                                            ggCAGCCAGTTCCGCCGCCAGGGCGCGGAATTTGCTGTCACGTTCACCACATAAATAAT‑AAACGCAAATGTGCGGGCGCTAAGGTTAGCACGTAAATCAGGCTGGACGGCGAGAGAAGTCGCCTCCAGCATGGCGGCAAg                                                        >  2:331051/1‑140 (MQ=255)

                                                                 ccAGTTCCGCCGCCAGGGCGCGGAATTTGCTGTCACGTTCACCACATAAATAAT‑AAACGCAAATGTGCGGGCGCTAAGGTTAGCACGTAAATCAGGCTGGACGGCGAGAGAAGTCGCCTCCAGCATGGCGGCAAGCGTTg                                                   <  2:146174/140‑1 (MQ=255)

                                                                     ttCCGCCGCCAGGGCGCGGAATTTGCTGTCACGTTCACCACATAAATAAT‑AAACGCAAATGTGCGGGCGCTAAGGTTAGCACGTAAATCAGGCTGGACGGCGAGAGAAGTCGCCTCCAGCATGGCGGCAAGCGTTGCGcc                                               <  1:55294/140‑1 (MQ=255)

                                                                             ccAGGGCGCGGAATTTGCTGTCACGTTCACCACATAAATAAT‑AAACGCAAATGTGCGGGCGCTAAGGTTAGCACGTAAATCAGGCTGGACGGCGAGAGAAGTCGCCTCCAGCATGGCGGCAAGCGTTGCGCCATTAttgt                                       >  1:98777/1‑140 (MQ=255)

                                                                                       gAATTTGCTGTCACGTTCACCACATAAATAAT‑AAACGCAAATGTGCGGGCGCTAAGGTTAGCACGTAAATCAGGCTGGACGGCGAGAGAAGTCGCCTCCAGCATGGCGGCAAGCGTTGCGCCATTATTGTTGCTGCGCAg                             >  1:13635/1‑140 (MQ=255)

                                                                                                           cacaTAAATAAT‑AAACGCAAATGTGCGGGCGCTAAGGTTAGCACGTAAATCAGGCTGGACGGCGAGAGAAGTCGCCTCCAGCATGGCGGCAAGCGTTGCGCCATTATTGTTGCTGCGCAGCGCCACCAGCTCCCGGCGtt         <  2:104561/140‑1 (MQ=255)

                                                                                                             caTAAATAAT‑AAACGCAAATGTGCGGGCGCTAAGGTTAGCACGTAAATCAGGCTGGACGGCGAGAGAAGTCGCCTCCAGCATGGCGGCAAGCGTTGCGCCATTATTGTTGCTGCGCAGCGCCACCAGCTCCCGGCGTTGa       >  1:8801/1‑140 (MQ=255)

                                                                                                              ataaataaT‑AAACGCAAATGTGCGGGCGCTAAGGTTAGCACGTAAATCAGGCTGGACGGCGAGAGAAGTCGCCTCCAGCATGGCGGCAAGCGTTGCGCCATTATTGTTGCTGCGCAGCGCCACCAGCTCCCGGCGTTGAt      <  1:331051/140‑1 (MQ=255)

                                                                                                               taaataaT‑AAACGCAAATGTGCGGGCGCTAAGGTTAGCACGTAAATCAGGCTGGACGGCGAGAGAAGTCGCCTCCAGCATGGCGGCAAGCGTTGCGCCATTATTGTTGCTGCGCAGCGCCACCAGCTCCCGGCGTTGATc     <  2:340792/140‑1 (MQ=255)

                                                                                                               taaataaT‑AAACGCAAATGTGCGGGCGCTAAGGTTAGCACGTAAATCAGGCTGGACGGCGAGAGAAGTCGCCTCCAGCATGGCGGCAAGCGTTGCGCCATTATTGTTGCTGCGCAGCGCCACCAGCTCCCGGCGTTGATc     <  2:8801/140‑1 (MQ=255)

                                                                                                                  ataat‑aAACGCAAATGTGCGGGCGCTAAGGTTAGCACGTAAATCAGGCTGGACGGCGAGAGAAGTCGCCTCCAGCATGGCGGCAAGCGTTGCGCCATTATTGTTGCTGCGCAGCGCCACCAGCTCCCGGCGTTGATCGTc  >  2:353830/1‑140 (MQ=255)

TACGCCAGCGGGATTTTCCCGATGCGCGTTATGTCCGGCGCGAGGAATGACATGGCAGTCGGCAGCCAGTTCCGCCGCCAGGGCGCGGAATTTGCTGTCACGTTCACCACATAAATAATAAAACGCAAATGTGCGGGCGCTAAGGTTAGCACGTAAATCAGGCTGGACGGCGAGAGAAGTCGCCTCCAGCATGGCGGCAAGCGTTGCGCCATTATTGTTGCTGCGCAGCGCCACCAGCTCCCGGCGTTGATCGTC  >  NC_000913/2376867‑2377121

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A