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 F1 I1 R1	182	31.9	1789978	98.5%	1763128	80.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,362,820	C→T	T5M (ACG→ATG)	yhcD →	putative fimbrial usher protein YhcD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,362,820	0	C	T	100.0%	55.2 / NA	16	T5M (ACG→ATG)	yhcD	putative fimbrial usher protein YhcD
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (10/6); total (10/6)

ATAAATATGTCACTGACTTAAAATAACTTTGCCTGGAGCGACAAGGATGTTAAAAAAAACGTTACTGGCCTACACCATTGGTTTTGCCTTTTCTCCCCCAGCCAATGCAGATGGTATAGAGATTGCCGCTG  >  NC_000913/3362761‑3362891

ataaataTGTCACTGACTTAAAATAACTTTGCCTGGAGCGACAAGGATGTTAAAAAAAATGTTACTGGCCTACACCATTg                                                     <  1:585071/80‑1 (MQ=255)

       tGTCACTGACTTAAAATAACTTTGCCTGGAGCGACAAGGATGTTAAAAAAAATGTTACTGGCCTACACCATTGGTTTTGc                                              <  1:585072/80‑1 (MQ=255)

              gACTTAAAATAACTTTGCCTGGAGCGACAAGGATGTTAAAAAAAGTGATACTGGCCTACACCAGTGGTTTTGCCTTTtctc                                      >  1:585084/1‑81 (MQ=255)

                   aaaaTAACTTTGCCTGGAGCGACAAGGATGTTAAAAAAAATGTTACTGGCCTACACCATTGGTTTTGCCTTTTCTccccc                                  <  2:585073/80‑1 (MQ=255)

                       tAACTTTGCCTGGAGCGACAAGGATGTTAAAAAAAATGTTACTGGCCTACACCATTGGTTTTGCCTTTTCTCCCCCAGcc                              >  2:585090/1‑80 (MQ=255)

                       tAACTTTGCCTGGAGCGACAAGGATGTTAAAAAAAATGTTACTGGCCTACACCATTGGTTTTGCCTTTTCTCCCCCAGCCa                             <  1:585074/81‑1 (MQ=255)

                               ccTGGAGCGACAAGGATGTTAAAAAAAATGTTACTGGCCTACACCATTGGTTTTGCCTTTTCTCCCCCAGCCAATGCAGAt                     <  2:585075/81‑1 (MQ=255)

                                 tGGAGCGACAAGGATGTTAAAAAAAATGTTACTGGCCTACACCATTGGTTTTGCCTTTTCTCCCCCAGCCAATGCAGATgg                   >  1:585088/1‑81 (MQ=255)

                                    aGCGACAAGGATGTTAAAAAAAATGTTACTGGCCTACACCATTGGTTTTGCCTTTTCTCCCCCAGCCAATGCAGATGGta                 >  1:585086/1‑80 (MQ=255)

                                      cGACAAGGATGTTAAAAAAAATGTTACTGGCCTACACCATTGGTTTTGCCTTTTCTCCCCCAGCCAATGCAGATGGta                 >  1:585089/1‑78 (MQ=255)

                                      cGACAAGGATGTTAAAAAAAATGTTACTGGCCTACACCATTGGTTTTGCCTTTTCTCCCCCAGCCAATGCAGATGGta                 >  2:585091/1‑78 (MQ=255)

                                      cGACAAGGATGTTAAAAAAAATGTTACTGGCCTACACCATTGGTTTTGCCTTTTCTCCCCCAGCCAATGCAGATGGta                 >  2:585093/1‑78 (MQ=255)

                                         cAAGGATGTTAAAAAAAATGTTACTGGCCTACACCATTGGTTTTGCCTTTTCTCCCCCAGCCAATGCAGATGGtata               >  2:585095/1‑77 (MQ=255)

                                                gTTAAAAAAAATGTTACTGGCCTACACCATTGGTTTTGCCTTTTCTCCCCCAGCCAATGCAGATGGTATAGAGATTGCCGc    >  1:585083/1‑81 (MQ=255)

                                                 ttAAAAAAAATGTTACTGGCCTACACCATTGGTTTTGCCTTTTCTCCCCCAGCCAATGCAGATGGTATAGAGATTGCCGc    <  1:585076/80‑1 (MQ=255)

                                                  tAAAAAAAATGTTACTGGCCTACACCATTGGTTTTGCCTTTTCTCCCCCAGCCAATGCAGATGGTATAGAGATTGCCGCTg  >  2:585092/1‑81 (MQ=255)

ATAAATATGTCACTGACTTAAAATAACTTTGCCTGGAGCGACAAGGATGTTAAAAAAAACGTTACTGGCCTACACCATTGGTTTTGCCTTTTCTCCCCCAGCCAATGCAGATGGTATAGAGATTGCCGCTG  >  NC_000913/3362761‑3362891

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A