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
A1 F2 I205 R1	220	17.5	961422	97.1%	933540	86.5

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	1,761,086	A→C	R619R (CGT→CGG)	ydiJ ←	FAD‑binding and (Fe‑S)‑binding domain‑containing protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,761,086	0	A	C	90.0%	26.2 / ‑4.7	10	R619R (CGT→CGG)	ydiJ	FAD‑binding and (Fe‑S)‑binding domain‑containing protein
Reads supporting (aligned to +/- strand): ref base A (0/1); new base C (3/6); total (3/7)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACGTCCGCAAACTGACGCCGGATTCAGGCAGTTCTTGTTCCAGTTTGAGTGGATCAACGCCGCGATCCGCCAACAAACGCAGCCATTCACGCACCAGCGTTGCGCGCCCTTTCGGTGAATGAATCCGGTTCTGGGTGATCTTCATCGACGGACA  >  NZ_CP009273/1761010‑1761163

aCGTCCGCAAACTGACGCCGGATTCAGGCAGTTCTTGTTCCAGTTTGAGTGGATCAACGCCGCGATCCGCCAACAAACGCAGCCATTCAc                                                                  <  1:309800/90‑1 (MQ=255)

  gTCCGCAAACTGACGCCGGATTCAGGCAGTTCTTGTTCCAGTTTGAGTGGATCAACGCCGCGATCCGCCAACAACCGCAGCCATTCACGc                                                                >  1:471467/1‑90 (MQ=255)

      gCAAACTGACGCCGGATTCAGGCAGTTCTTGTTCCAGTTTGAGTGGATCAACGCCGCGATCCGCCAACAACCGCAGCCATTCACGCACCa                                                            >  1:439302/1‑90 (MQ=255)

               cGCCGGATTCAGGCAGTTCTTGTTCCAGTTTGAGTGGATCAACGCCGCGATCCGCCAACAACCGCAGCCATTCACGCACCAGCGTTgcgc                                                   <  1:428150/90‑1 (MQ=255)

                 ccGGATTCAGGCAGTTCTTGTTCCAGTTTGAGTGGATCAACGCCGCGATCCGCCAACAACCGCAGCCATTCACGCACCAGCGTTgcgcgc                                                 <  1:463561/90‑1 (MQ=255)

                 ccGGATTCAGGCAGTTCTTGTTCCAGTTTGAGTGGATCAACGCCGCGATCCGCCAACAACCGCAGCCATTCACGCACCAGCGTTgcgcgc                                                 <  2:146213/90‑1 (MQ=255)

                                        cAGTTTGAGTGGATCAACGCCGCGATCCGCCAACAACCGCAGCCATTCACGCACCAGCGTTGCGCGCCCTTTCGGTGAATGAATCCGGtt                          >  2:167285/1‑90 (MQ=255)

                                                          gccgcGATCCGCCAACAACCGCAGCCATTCACGCACCAGCGTTGCGCGCCCTTTCGGTGAATGAATCCGGTTCTGGGTGATCTTCATCGa        <  1:167890/90‑1 (MQ=255)

                                                          gccgcGATCCGCCAACAACCGCAGCCATTCACGCACCAGCGTTGCGCGCCCTTTCGGTGAATGAATCCGGTTCTGGGTGATCTTCATCGa        <  2:56975/90‑1 (MQ=255)

                                                                aTCCGCCAACAACCGCAGCCATTCACGCACCAGCGTTGCGCGCCCTTTCGGTGAATGAATCCGGTTCTGGGTGATCTTCATCgacagaca  <  1:466918/90‑1 (MQ=255)

ACGTCCGCAAACTGACGCCGGATTCAGGCAGTTCTTGTTCCAGTTTGAGTGGATCAACGCCGCGATCCGCCAACAAACGCAGCCATTCACGCACCAGCGTTGCGCGCCCTTTCGGTGAATGAATCCGGTTCTGGGTGATCTTCATCGACGGACA  >  NZ_CP009273/1761010‑1761163

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 19 ≤` `ATCG/ATCG` `< 31 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

BRESEQ :: bam2aln output

GGCAATTAACGTCCGCAAACTGACGCCGGATTCAGGCAGTTCTTGTTCCAGTTTGAGTGGATCAACGCCGCGATCCGCCAACAAACGCAGCCATTCACGCACCAGCGTTGCGCGCCCTTTCGGTGAATGAATCCGGTTCTGGGTGATCTTCATCGACGGACACATCGGACTACGGGCATCA  >  NZ_CP009273/1761002‑1761182

GGCAATTAACGTCCGCAAACTGACGCCGGATTCAGGCAGTTCTTGTTCCAGTTTGAGTGGATCAACGCCGCGATCCGCCAACAACCGCAGCCATTCACGC                                                                                   >  SRR3722087.476954/1‑100 (MQ=60)

    ATTAACGTCCGCAAACTGACGCCGGATTCAGGCAGTTCTTGTTCCAGTTTGAGTGGATCAACGCCGCGATCCGCCAACAACCGCAGCCATTCACGCACCA                                                                               >  SRR3722087.444445/1‑100 (MQ=60)

        ACGTCCGCAAACTGACGCCGGATTCAGGCAGTTCTTGTTCCAGTTTGAGTGGATCAACGCCGCGATCCGCCAACAAACGCAGCCATTCACGCACCAGCGT                                                                           <  SRR3722087.313055/100‑1 (MQ=60)

                       CGCCGGATTCAGGCAGTTCTTGTTCCAGTTTGAGTGGATCAACGCCGCGATCCGCCAACAACCGCAGCCATTCACGCACCAGCGTTGCGCGCCCTTTCGG                                                            <  SRR3722087.433144/100‑1 (MQ=60)

                         CCGGATTCAGGCAGTTCTTGTTCCAGTTTGAGTGGATCAACGCCGCGATCCGCCAACAACCGCAGCCATTCACGCACCAGCGTTGCGCGCCCTTTCGGTG                                                          <  SRR3722087.468957/100‑1 (MQ=60)

                                                                  GCCGCGATCCGCCAACAACCGCAGCCATTCACGCACCAGCGTTGCGCGCCCTTTCGGTGAATGAATCCGGTTCTGGGTGATCTTCATCGACGGACACATC                 <  SRR3722087.169418/100‑1 (MQ=60)

                                                                        ATCCGCCAACAACCGCAGCCATTCACGCACCAGCGTTGCGCGCCCTTTCGGTGAATGAATCCGGTTCTGGGTGATCTTCATCGACAGACACATCGGACTA           <  SRR3722087.472344/100‑1 (MQ=60)

                                                                                 CAACCGCAGCCATTCACGCACCAGCGTTGCGCGCCCTTTCGGTGAATGAATCCGGTTCTGGGTGATCTTCATCGACGGACACATCGGACTACGGGCATCA  >  SRR3722087.53329/1‑100 (MQ=60)

GGCAATTAACGTCCGCAAACTGACGCCGGATTCAGGCAGTTCTTGTTCCAGTTTGAGTGGATCAACGCCGCGATCCGCCAACAAACGCAGCCATTCACGCACCAGCGTTGCGCGCCCTTTCGGTGAATGAATCCGGTTCTGGGTGATCTTCATCGACGGACACATCGGACTACGGGCATCA  >  NZ_CP009273/1761002‑1761182

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 18 ≤` `ATCG/ATCG` `< 30 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`