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 F28 I3 R2	122	64.1	3058059	97.6%	2984665	63.3

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	minE	692,900	T→C	A144A (GCT→GCC)	hyaD →	protein involved in processing of HyaA and HyaB proteins

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	692,900	0	T	C	100.0%	107.1 / NA	32	A144A (GCT→GCC)	hyaD	protein involved in processing of HyaA and HyaB proteins
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (15/17); total (15/17)

CAACCCGCAATGCTCGACGACTACGGCGGTAGCCTGAGCGAACTGGCACGGGAGCAACTGCCCGCTGCGGAACAGGCGGCGCTGGCGCAGCTTGCTGCGTGGGGAATTGTGCCGCAACCGGCTAATGAAT  >  minE/692835‑692964

cAACCCGCAATGCTCGACGACTACGGCGGTAGCCTGAGCGAACTGGCACGGGAGCAACTGCCCGCCGCgg                                                              <  1:871991/70‑1 (MQ=255)

     cGCAATGCTCGACGACTACGGCGGTAGCCTGAGCGAACTGGCACGGGAGCAACTGCCCGCCGCgg                                                              <  1:1682651/65‑1 (MQ=255)

     cGCAATGCTCGACGACTACGGCGGTAGCCTGAGCGAACTGGCACGGGAGCAACTGCCCGCCGCGGAACAgg                                                        <  1:1896528/71‑1 (MQ=255)

      gCAATGCTCGACGACTACGGCGGTAGCCTGAGCGAACTGGCACGGGAGCAACTGCCCGCCGCGGAACAggc                                                       <  1:1282444/71‑1 (MQ=255)

           gCTCGACGACTACGGCGGTAGCCTGAGCGAACTGGCACGGGAGCAACTGCCCGCCGCGGAACAGGCGgcgc                                                  >  1:1937048/1‑71 (MQ=255)

            cTCGACGACTACGGCGGTAGCCTGAGCGAACTGGCACGGGAGCAACTGCCCGCCGCGGAACAGGCGgcgc                                                  <  1:610052/70‑1 (MQ=255)

             tCGACGACTACGGCGGTAGCCTGAGCGAACTGGCACGGGAGCAACTGCCCGCCGCGGAACAGGCGGCGCTg                                                >  1:429211/1‑71 (MQ=255)

                  gacTACGGCGGTAGCCTGAGCGAACTGGCACGGGAGCAACTGCCCGCCGCGGAACAGGCGGCGCTGgcg                                             >  1:652995/1‑69 (MQ=255)

                  gacTACGGCGGTAGCCTGAGCGAACTGGCACGGGAGCAACTGCCCGCCGCGGAACAGGCGGCGCTGgcg                                             >  1:2199281/1‑69 (MQ=255)

                       cggcggTAGCCTGAGCGAACTGGCACGGGAGCAACTGCCCGCCGCGGAACa                                                          >  1:968585/1‑51 (MQ=255)

                       cggcggTAGCCTGAGCGAACTGGCACGGGAGCAACTGCCCGCCGCGGAACAGGCGGCGCTGGCGCAGCtt                                       <  1:318408/70‑1 (MQ=255)

                       cggcggTAGCCTGAGCGAACTGGCACGGGAGCAACTGCCCGCCGCGGAACAGGCGGCGCTGGCGCAGCTtg                                      >  1:965082/1‑71 (MQ=255)

                       cggcggTAGCCTGAGCGAACTGGCACGGGAGCAACTGCCCGCCGCGGAACAGGCGGCGCTGGCGCAGCTtg                                      <  1:69136/71‑1 (MQ=255)

                        ggcggTAGCGTGAGCGAACTGGCACGGGAGCAACTGCCCGCCGCGGAACAGGCGGCGCTGGCGCa                                           <  1:1473876/65‑1 (MQ=255)

                         gcggTAGCCTGAGCGAACTGGCACGGGAGCAACTGCCCGCCGCGGAACAGGCGGCGCTGGCGCAGCTtgct                                    <  1:2280334/71‑1 (MQ=255)

                          cggTAGCCTGAGCGAACTGGCACGGGAGCAACTGCCCGCCGCGGAACAGGCGGCGCTGGCGCAGCTtgctg                                   >  1:2855348/1‑71 (MQ=255)

                               gCCTGAGCGAACTGGCACGGGAGCAACTGCCCGCCGCGGAACAGGCGGCGCTGGCGCAGCTTGCTGCGt                                <  1:1166039/69‑1 (MQ=255)

                                 cTGAGCGAACTGGCACGGGAGCAACTGCCCGCCGCGGAACAGGCGGCGCTGGCGCAGCTTGCTGCGTgggg                            <  1:1282095/71‑1 (MQ=255)

                                  tGAGCGAACTGGCACGGGAGCAACTGCCCGCCGCGGAACAGGCGGCGCTGGCGCAGc                                         <  1:94482/57‑1 (MQ=255)

                                        aaCTGGCACGGGAGCAACTGCCCGCCGCGGAACAGGCGGCGCTGGCGCAGCTTGCTGCGTGCGGAATtgtg                     >  1:871956/1‑71 (MQ=255)

                                         aCTGGCACGGGAGCAACTGCCCGCCGCGGAACAGGCGGCGCTGGCGCAGCTTGCTGCGTGGGGAATtgtg                     >  1:934485/1‑70 (MQ=255)

                                         aCTGGCACGGGAGCAACTGCCCGCCGCGGAACAGGCGGCGCTGGCGCAGCTTGCTGCGTGGGGAATTGTGc                    >  1:933742/1‑71 (MQ=255)

                                            ggCACGGGAGCAACTGCCCGCCGCGGAACAGGCGGCGCTGGCGCAGCTTGCTGCGTGGGGAATTGTGCCg                  >  1:1462580/1‑70 (MQ=255)

                                             gCACGGGAGCAACTGCCCGCCGCGGAACAGGCGGCGCTGGCGCAGCTTGCTGCGTGGGGAATTGTGCCg                  <  1:27076/69‑1 (MQ=255)

                                               aCGGGAGCAACTGCCCGCCGCGGAACAGGCGGCGCTGGCGCAGCTTGCTGCGTGGGGAATTGTGCCGCAAc              <  1:2192797/71‑1 (MQ=255)

                                               aCGGGAGCAACTGCCCGCCGCGGAACAGGCGGCGCTGGCGCAGCTTGCTGCGTGGGGAATTGTGCCGCAAc              <  1:2174899/71‑1 (MQ=255)

                                                cGGGAGCAACTGCCCGCCGCGGAACAGGCGGCGCTGGCGCAGCTTGCTGCGTGGGGAATTGTGCCGCAAcc             >  1:1230637/1‑71 (MQ=255)

                                                 gggAGCAACTGCCCGCCGCGGAACAGGCGGCGCTGGCGCAGCTTGCTGCGTGGGGAATTGTGCCGCAACCg            >  1:886295/1‑71 (MQ=255)

                                                    aGCAACTGCCCGCCGCGGAACAGGCGGCGCTGGCGCAGCTTGCTGCGTGGGGAATTGTGCCGCAACCGGCt         <  1:137818/71‑1 (MQ=255)

                                                            cccGCCGCGGAACAGGCGGCGCTGGCGCAGCTtgctgc                                  >  1:1957366/1‑38 (MQ=255)

                                                            cccGCCGCGGAACAGGCGGCGCTGGCGCAGCTTGCTGCGTGGGGAATTGTGCCGCAACCGGCTAATGaa   <  1:3029882/69‑1 (MQ=255)

                                                            cccGCCGCGGAACAGGCGGCGCTGGCGCAGCTTGCTGCGTGGGGAATTGTGCCGCAACCGGCTAATGAAt  >  1:803935/1‑70 (MQ=255)

CAACCCGCAATGCTCGACGACTACGGCGGTAGCCTGAGCGAACTGGCACGGGAGCAACTGCCCGCTGCGGAACAGGCGGCGCTGGCGCAGCTTGCTGCGTGGGGAATTGTGCCGCAACCGGCTAATGAAT  >  minE/692835‑692964

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A