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	155	25.8	2285122	88.0%	2010907	104.3

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	AM260479	1,492,953	T→G	S201A (TCA→GCA)	pdhB →	dihydrolipoamide acetyltransferase (E2) component of pyruvate dehydrogenase complex

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	AM260479	1,492,953	0	T	G	100.0%	40.5 / NA	12	S201A (TCA→GCA)	pdhB	dihydrolipoamide acetyltransferase (E2) component of pyruvate dehydrogenase complex
Reads supporting (aligned to +/- strand): ref base T (0/0); new base G (7/5); total (7/5)

TGGACGTGCCGTCGCCGCAAGGCGGCGTGGTCAAGGAAGTCAAGGTCAAGGTCGGTGACAACGTCGCCGAAGGCACGTTGCTGCTGATCCTGGAAGGCGCCGCCGCATCAGCCGCCCCGGCAGCTGCCGCCGCGGCACCGGCTCCGGCTGCCAGCGCGCCCGCACCGGCACCGGCCCCCGCAGCCGCCGCCCCGGCACCGGCCGCAGCACCTGCTGCCGCGCCGGCC  >  AM260479/1492846‑1493072

tGGACGTGCCGTCGCCGCAAGGCGGCGTGGTCAAGGAAGTCAAGGTCAAGGTCGGTGACAACGTCGCCGAAGGCACGCTGCTGCTGATCCTGGAAGGCGCCGCCGCAGCAGCCGCCCCGGCAGCTGCCGCcgcg                                                                                               >  2:64263/1‑134 (MQ=255)

        ccGTCGCCGCAAGGCGGCGTGGTCAAGGAAGTCAAGGTCAAGGTCGGTGACAACGTCGCCGAAGGCACGCTGCTGCTGATCCTGGAAGGCGCCGCCGCAGCAGCCGCCCCGGCAGCTGCCGCCGCGGCAccggc                                                                                       >  1:526948/1‑134 (MQ=255)

                                                aggtcGGTGACAACGTCGCCGAAGGCACGCTGCTGCTGATCCTGGAAGGCGCCGCCGCAGCAGCCGCCCCGGCAGCTGCCGCCGCGGCACCGGCTCCGGCTGCCAGCGCGCCCGCACCGGCACCGGCCCCCg                                                 >  1:1122586/1‑132 (MQ=255)

                                                          cAACGTCGCCGAAGGCACGCTGCTGCTGATCCTGGAAGGCGCCGCCGCAGCAGCCGCCCCGGCAGCTGCCGCCGCGGCACCGGCTCCGGCTGCCAGCGCGCCCGCACCGGCACCGGCCCCCGCAGCCGCCGccc                                     >  2:428051/1‑134 (MQ=255)

                                                           aaCGTCGCCGAAGGCACGCTGCTGCTGATCCTGGAAGGCGCCGCCGCAGCAGCCGCCCCGGCAGCTGCCGCCGCGGCACCGGCTCCGGCTGCCAGCGCGCCCGCACCGGCACCGGCCCCCGCAGCCGCCGcccc                                    <  1:64263/134‑1 (MQ=255)

                                                                cGCCGAAGGCACGCTGCTGCTGATCCTGGAAGGCGCCGCCGCAGCAGCCGCCCCGGCAGCTgccg                                                                                                    >  1:808247/1‑65 (MQ=39)

                                                                cGCCGAAGGCACGCTGCTGCTGATCCTGGAAGGCGCCGCCGCAGCAGCCGCCCCGGCAGCTgccg                                                                                                    <  2:808247/65‑1 (MQ=39)

                                                                                             aaGGCGCCGCCGCAGCAGCCGCCCCGGCAGCTGCCGCCGCGGCACCGGCTCCGGCTGCCAGCGCGCCCGCACCGGCACCGGCCCCCGCAGCCGCCGCCCCGGCACCGGCCGCAGCACCTGCTGCCGCgccggcc  <  2:1122586/134‑1 (MQ=255)

                                                                                                     gccgcAGCAGCCGCCCCGGCAGCTGCCGCCGCGGCACCGGCTCCGGCTGCCAGCGCGccc                                                                    >  1:659447/1‑60 (MQ=255)

                                                                                                     gccgcAGCAGCCGCCCCGGCAGCTGCCGCCGCGGCACCGGCTCCGGCTGCCAGCGCGccc                                                                    <  2:659447/60‑1 (MQ=255)

                                                                                                     gccgcAGCAGCCGCCCCGGCAGCTGCCGCCGCGGCACCGGCTCCGGCTGCCAGCGCGCCCGCACCGGCACCGGCCCCCGCAg                                              <  1:419805/82‑1 (MQ=255)

                                                                                                     gccgcAGCAGCCGCCCCGGCAGCTGCCGCCGCGGCACCGGCTCCGGCTGCCAGCGCGCCCGCACCGGCACCGGCCCCCGCAg                                              >  2:419805/1‑82 (MQ=255)

TGGACGTGCCGTCGCCGCAAGGCGGCGTGGTCAAGGAAGTCAAGGTCAAGGTCGGTGACAACGTCGCCGAAGGCACGTTGCTGCTGATCCTGGAAGGCGCCGCCGCATCAGCCGCCCCGGCAGCTGCCGCCGCGGCACCGGCTCCGGCTGCCAGCGCGCCCGCACCGGCACCGGCCCCCGCAGCCGCCGCCCCGGCACCGGCCGCAGCACCTGCTGCCGCGCCGGCC  >  AM260479/1492846‑1493072

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

BRESEQ :: bam2aln output

GCCACCATGGACGTGCCGTCGCCGCAAGGCGGCGTGGTCAAGGAAGTCAAGGTCAAGGTCGGTGACAACGTCGCCGAAGGCACGTTGCTGCTGATCCTGGAAGGCGCCGCCGCATCAGCCGCCCCGGCAGCTGCCGCCGCGGCACCGGCTCCGGCTGCCAGCGCGCCCGCACCGGCACCGGCCCCCGCAGCCGCCGCCCCGGCACCGGCCGCAGCACCTGCTGCCGCGCCGGCCGCCGCTGGC  >  AM260479/1492839‑1493081

GCCACCATGGACGTGCCGTCGCCGCAAGGCGGCGTGGTCAAGGAAGTCAAGGTCAAGGTCGGTGACAACGTCGCCGAAGGCACGCTGCTGCTGATCCTGGAAGGCGCCGCCGCAGCAGCCGCCCCGGCAGCTGCCGCCGCGGCACCGGCT                                                                                               >  GWNJ‑0478:712:GW2002102894th:2:1215:11073:65668/1‑150 (MQ=60)

                         AAGGCGGCGTGGTCAAGGAAGTCAAGGTCAAGGCCGGTGACAACGTCGCCGAAGGCACGCTGCTGCTGATCCTGGAAGGCGCCGCCGCAGCAGCCGCCCCGGCAGCTGCggcggcgccttccaggatcagcagcagcgtgccttcggcga                                                                      <  GWNJ‑0478:712:GW2002102894th:2:1215:6767:84915/150‑42 (MQ=60)

                                        AGGAAGTCAAGGTCAAGGTCGGTGACAACGTCGCCGAAGGCACGCTGCTGCTGATCCTGGAAGGCGCCGCCGCAGCAGCCGCCCCGGCAGCTGCCGCCGCGGCACCGGCTCCGGCTGCCAGCGCGCCCGCACCGGCACCGGCCCCCGC                                                         >  GWNJ‑0478:712:GW2002102894th:2:2216:13609:3666/1‑148 (MQ=60)

                                                       gagtgtctcgtgggctcggagatgtgtataagagacaGATCCTGGAAGGCGCCGCCGCAGCAGCCGCCCCGGCAGCTGCCGCCGCGGCACCGGCTCCGGCTGCCAGCGCGCCCGCACCGGCACCGGCCCCCGCAGCCGCCGCCCCGGCAC                                        <  GWNJ‑0478:712:GW2002102894th:2:1209:15363:21819/113‑1 (MQ=60)

                                                        GGTCGGTGACAACGTCGCCGAAGGCACGCTGCTGCTGATCCTGGAAGGCGCCGCCGCAGCAGCCGCCCCGGCAGCTGCCGCCGCGGCACCGGCTCCtgtctcttatacacatctccgagcccacgagacactcgctaatctcgtatgccg                                       >  GWNJ‑0478:712:GW2002102894th:2:2115:7676:63338/1‑96 (MQ=60)

                                                                 CAACGTCGCCGAAGGCACGCTGCTGCTGATCCTGGAAGGCGCCGCCGCAGCAGCCGCCCCGGCAGCTGCCGCCGCGGCACCGGCTCCGGCTGCCAGCGCGCCCGCACCGGCACCGGCCCCCGCAGCCGCCGCCCCGGCACCGGCCGCAGC                              <  GWNJ‑0478:712:GW2002102894th:2:1104:16725:8555/150‑1 (MQ=60)

                                                                                             ATCCTGGAAGGCGCCGCCGCAGCAGCCGCCCCGGCAGCTGCCGCCGCGGCACCGGCTCCGGCTGCCAGCGCGCCCGCACCGGCACCGGCCCtgtctcttatacacatctccgagcccacgagacactcgctaatctcgtatgccgtcttc  >  GWNJ‑0478:712:GW2002102894th:2:2107:8445:45159/1‑91 (MQ=60)

GCCACCATGGACGTGCCGTCGCCGCAAGGCGGCGTGGTCAAGGAAGTCAAGGTCAAGGTCGGTGACAACGTCGCCGAAGGCACGTTGCTGCTGATCCTGGAAGGCGCCGCCGCATCAGCCGCCCCGGCAGCTGCCGCCGCGGCACCGGCTCCGGCTGCCAGCGCGCCCGCACCGGCACCGGCCCCCGCAGCCGCCGCCCCGGCACCGGCCGCAGCACCTGCTGCCGCGCCGGCCGCCGCTGGC  >  AM260479/1492839‑1493081

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 15 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`