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
A0 F0 I1 R1	87	31.3	1776092	98.2%	1744122	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%	65.0 / NA	18	T5M (ACG→ATG)	yhcD	putative fimbrial usher protein YhcD
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (9/9); total (9/9)

ATATGGTTATCGCGGTAATAAATATGTCACTGACTTAAAATAACTTTGCCTGGAGCGACAAGGATGTTAAAAAAAACGTTACTGGCCTACACCATTGGTTTTGCCTTTTCTCCCCCAGCCAATGCAGATGGTATAGAGATTGCCGCTGTTGATT  >  NC_000913/3362744‑3362897

atatGGTTATCGCGGTAATAAATATGTCACTGACTTAAAATAACTTTGCCTGGAGCGACAAGGATGTTAAAAAAAATGTTa                                                                           <  1:613621/81‑1 (MQ=255)

   tGGTTATCGCGGTAATAAATATGTCACTGACTTAAAATAACTTTGCCTGGAGCGACAAGGATGTTAAAAAAAATGTTACt                                                                         <  1:613622/80‑1 (MQ=255)

      ttATCGCGGTAATAAATATGTCACTGACTTAAAATAACTTTGCCTGGAGCGACAAGGATGTTAAAAAAAATGTTACTGGcc                                                                     >  1:613643/1‑81 (MQ=255)

        aTCGCGGTAATAAATATGTCACTGACTTAAAATAACTTTGCCTGGAGCGACAAGGATGTTAAAAAAAATGTTACTGGCCTa                                                                   >  2:613647/1‑81 (MQ=255)

             ggTAATAAATATGTCACTGACTTAAAATAACTTTGCCTGGAGCGACAAGGATGTTAAAAAAAATGTTACTGGCCTACACCa                                                              >  2:613657/1‑81 (MQ=255)

                    aataTGTCACTGACTTAAAATAACTTTGCCTGGAGCGACAAGGATGTTAAAAAAAATGTTACTGGCCTACACCATTGGtt                                                        <  2:613623/80‑1 (MQ=255)

                                aCTTAAAATAACTTTGCCTGGAGCGACAAGGATGTTAAAAAAAATGTTACTGGCCTACACCATTGGTTTTGCCTTTtctc                                            <  1:613624/80‑1 (MQ=255)

                                 cTTAAAATAACTTTGCCTGGAGCGACAAGGATGTTAAAAAAAATGTTACTGGCCTACACCATTGGTTTTGCCTTTTCTccc                                          <  1:613625/81‑1 (MQ=255)

                                    aaaaTAACTTTGCCTGGAGCGACAAGGATGTTAAAAAAAATGTTACTGGCCTACACCATTGGTTTTGCCTTTTCTcccc                                         >  2:613650/1‑79 (MQ=255)

                                     aaaTAACTTTGCCTGGAGCGACAAGGATGTTAAAAAAAATGTTACTGGCCTACACCATTGGTTTTGCCTTTTCTCCCCCa                                       <  1:613626/80‑1 (MQ=255)

                                             ttGCCTGGAGCGACAAGGATGTTAAAAAAAATGTTACTGGCCTACACCATTGGTTTTGCCTTTTCTCCCCCAGCCAATg                                >  2:613662/1‑79 (MQ=255)

                                                   ggAGCGACAAGGATGTTAAAAAAAATGTTACTGGCCTACACCATTGGTTTTGCCTTTTCTCCCCCAGCCAATGCAGATgg                         >  1:613652/1‑80 (MQ=255)

                                                    gAGCGACAAGGATGTTAAAAAAAATGTTACTGGCCTACACCATTGGTTTTGCCTTTTCTCCCCCAGCCAATGCAGATGGta                       >  2:613656/1‑81 (MQ=255)

                                                        gACAAGGATGTTAAAAAAAATGTTACTGGCCTACACCATTGGTTTTGCCTTTTCTCCCCCAGCCAATGCAGATGGtata                     >  2:613651/1‑79 (MQ=255)

                                                           aaGGATGTTAAAAAAAATGTTACTGGCCTACGCCATTGGTTTTGCCTTTTCTCCCCCAGCCAATGCAGATGGTATAGAGAt                <  2:613627/81‑1 (MQ=255)

                                                                  ttAAAAAAAATGTTACTGGCCTACACCATTGGTTTTGCCTTTTCTCCCCCAGCCAATGCAGATGGTATAGAGATTGCCGCt         <  1:613628/81‑1 (MQ=255)

                                                                     aaaaaaaTGTTACTGGCCTACACCATTGGTTTTGCCTTTTCTCCCCCAGCCAATGCAGATGGTATAGAGATTGCCGCTGtt      >  1:613659/1‑81 (MQ=255)

                                                                         aaaTGTTACTGGCCTACACCATTGGTTTTGCCTTTTCTCCCCCAGCCAATGCAGATGGTATAGAGATTGCCGCTGTTGAtt  <  2:613629/81‑1 (MQ=255)

ATATGGTTATCGCGGTAATAAATATGTCACTGACTTAAAATAACTTTGCCTGGAGCGACAAGGATGTTAAAAAAAACGTTACTGGCCTACACCATTGGTTTTGCCTTTTCTCCCCCAGCCAATGCAGATGGTATAGAGATTGCCGCTGTTGATT  >  NC_000913/3362744‑3362897

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A