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	149	26.7	2337422	87.5%	2045244	105.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	AM260479	275,969	+C	coding (268/558 nt)	h16_A0264 ←	Hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	AM260479	275,968	1	.	C	100.0%	42.2 / NA	12	A90G (GCC→GGC)	h16_A0264	Hypothetical protein
Reads supporting (aligned to +/- strand): ref base . (0/0); new base C (6/6); total (6/6)

CACCAGGGCTTGCAGCGCCCTGAAATAGCTATCCTTGCCTTCGAAGCGGCTGTAGAACGCGCCGGTCGTGACGCCGG‑CTGCGCGCAGATTTCCTGGATCGAGACCTGTTCCAGCGTGCGCTCGCAGCAGCCGGCGGCCGGCTTCCAGCAGCAGCAGCGTGGTGCGCAGGCCACGCGAATAGCGCGGTGCGATCC  >  AM260479/275892‑276085

cACCAGGGCTTGCAGCGCCCTGAAATAGCTATCCTTGCCTTCGAAGCGGCTGTAGAACGCGCCGGTCGTGACGCCGGCCTGCGCGCAGATTTCCTGGATCGAGACCTGTTCCAGCGTGCGCTCGCAGCAGCcgg                                                               <  2:775782/134‑1 (MQ=255)

         ttGCAGCGCCCTGAAATAGCTATCCTTGCCTTCGAAGCGGCTGTAGAACGCGCCGGTCGTGACGCCGGCCTGCGCGCAGATTTCCTGGATCGAGACCTGTTCCAGCGTGCGCTCGCAGCAGCCGGCGGCCGGCt                                                      >  2:909510/1‑134 (MQ=255)

                  ccTGAAATAGCTATCCTTGCCTTCGAAGCGGCTGTAGAACGCGCCGGTCGTGACGCCGGCCTGCGCGCAGATTTCCTGGATCGAGACCTGTTCCAGCGTGCGCTCGCAGCAGCCGGCGGCCGGCTTCcagcagc                                             <  1:909510/134‑1 (MQ=255)

                     gAAATAGCTATCCTTGCCTTCGAAGCGGCTGTAGAACGCGCCGGTCGTGACGCCGGCCTGCGCGCAGATTTCCTGGATCGAGACCTGTTCCAGCGTGCGCTCGCAGCAGCCGGCGGCCGGCTTCcagcagcag                                           >  2:1127735/1‑133 (MQ=255)

                                 cTTGCCTTCGAAGCGGCTGTAGAACGCGCCGGTCGTGACGCCGGCCTGCGCGCAGATTTCCTGGATCGAGACCTGTTCCAGCGTGCGCTCGCAGCAGCCGGCGGCCGGCTTCCAGCAGCAGCAGCGTGGTgcgc                              <  1:1127735/134‑1 (MQ=255)

                                    gCCTTCGAAGCGGCTGTAGAACGCGCCGGTCGTGACGCCGGCCTGCGCGCAGATTTCCTGGATCg                                                                                                <  1:462929/65‑1 (MQ=255)

                                    gCCTTCGAAGCGGCTGTAGAACGCGCCGGTCGTGACGCCGGCCTGCGCGCAGATTTCCTGGATCg                                                                                                >  2:462929/1‑65 (MQ=255)

                                                             ccGGTCGTGACGCCGGCCTGCGCGCAGATTTCCTGGATCGAGACCTGTTCCAGCGTGCGCTCGCAGCAGCCGGCGGCCGGCTTCCAGCAGCAGCAGCGTGGTGCGCAGGCCACGCGAATAGCGCGGTGCGATcc  >  1:506781/1‑134 (MQ=255)

                                                               ggTCGTGACGCCGGCCTGCGCGCAGATTTCCTGGATCGAGACCTGTTCCAGCGTGCGCTCGCAGCAGCcggcg                                                             >  1:431353/1‑73 (MQ=255)

                                                               ggTCGTGACGCCGGCCTGCGCGCAGATTTCCTGGATCGAGACCTGTTCCAGCGTGCGCTCGCAGCAGCcggcg                                                             <  2:431353/73‑1 (MQ=255)

                                                               ggTCGTGACGCCGGCCTGCGCGCAGATTTCCTGGATCGAGACCTGTTCCAGCGTGCGCTCGCAGCAGCCGGCGGCCGGCTTc                                                    >  1:686416/1‑82 (MQ=255)

                                                               ggTCGTGACGCCGGCCTGCGCGCAGATTTCCTGGATCGAGACCTGTTCCAGCGTGCGCTCGCAGCAGCCGGCGGCCGGCTTc                                                    <  2:686416/82‑1 (MQ=255)

CACCAGGGCTTGCAGCGCCCTGAAATAGCTATCCTTGCCTTCGAAGCGGCTGTAGAACGCGCCGGTCGTGACGCCGG‑CTGCGCGCAGATTTCCTGGATCGAGACCTGTTCCAGCGTGCGCTCGCAGCAGCCGGCGGCCGGCTTCCAGCAGCAGCAGCGTGGTGCGCAGGCCACGCGAATAGCGCGGTGCGATCC  >  AM260479/275892‑276085

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `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

GTTGCGCAAGCGGCTCGGCCATGCCCTTGCGCAGCGTGGCCAGCACCAGGGCTTGCAGCGCCCTGAAATAGCTATCCTTGCCTTCGAAGCGGCTGTAGAACGCGCCGGTCGTGACGCCGG‑CTGCGCGCAGATTTCCTGGATCGAGACCTGTTCCAGCGTGCGCTCGCAGCAGCCGGCGGCCGGCTTCCAGCAGCAGCAGCGTGGTGCGCAGGCCACGCGAATAGCGCGGTGCGATCCTCG  >  AM260479/275849‑276088

tattgatttgttgtatgttgttttttttttttttttcaagcagaagacggcatacgagattagcgagtgtctcgtgggctcggagatgtgtataagagacaGCGCCGGTCGTGACGCCGGCCTGCGCGCAGATTTCCTGGATCGAGACC                                                                                              <  GWNJ‑0478:712:GW2002102894th:2:2208:12628:12171/48‑1 (MQ=60)

         cggcatacgagattagcgagtgtctcgtgggctcggagatgtgtataagagacagGAAATAGCTATCCTTGCCTTCGAAGCGGCTGTAGAACGCGCCGGTCGTGACGCCGGCCTGCGCGCAGATTTCCTGGATCGAGACCTGTTCCAGCG                                                                                    <  GWNJ‑0478:712:GW2002102894th:2:1210:18403:61336/95‑1 (MQ=60)

                                     GGCCAGCACCAGGGCTTGCAGCGCCCTGAAATAGCTATCCTTGCCTTCGAAGCGGCTGTAGAACGCGCCGGACGTGACGCCGGCCTGCGCGCAGATTTCCTGGATCGAGACCGGTTCACGCGTGCGCTCGCAGCGGCCGGCGtcaccacc                                                        >  GWNJ‑0478:712:GW2002102894th:2:2207:1572:48927/1‑142 (MQ=60)

                                                           GCCCTGAAATAGCTATCCTTGCCTTCGAAGCGGCTGTAGAACGCGCCGGTCGTGACGCCGGCCTGCGCGCAGATTTCCTGctgtctcttatacacatctccgagcccacgagacactcgctaatctcgtatgccgtcttctgcttgaaa                                   >  GWNJ‑0478:712:GW2002102894th:2:2212:10374:32144/1‑80 (MQ=60)

                                                            CCCTGAAATAGCTATCCTTGCCTTCGAAGCGGCTGTAGAACGCGCCGGTCGTGACGCCGGCCTGCGCGCAGATTTCCTGGATCGAGACCTGTTCCAGCGTGCGCTCGCAGCAGCCGGCGGCCGGCTTCCAGCAGCAGCAGCGTGGTGCGC                                 <  GWNJ‑0478:712:GW2002102894th:2:2202:20239:51231/150‑1 (MQ=60)

                                                              CTGAAATAGCTATCCTTGCCTTCGAAGCGGCTGTAGAACGCGCCGGTCGTGACGCCGGCCTGCGCGCAGATTTCCTGctgtctcttatacacatctccgagcccacgagacactcgctaatctcgtatgccgtcttctgcttgaaaaaa                                >  GWNJ‑0478:712:GW2002102894th:2:1103:8796:44572/1‑77 (MQ=60)

                                                                       CTATCCTTGCCTTCGAAGCGGCTGTAGAACGCGCCGGTCGTGACGCCGGCCTGCGCGCAGATTTCCTGGATCGAGACCTGTTCCAGCGTGCGCTCGCAGCAGCCGGCGGCgcacctgccgtcgcgtgtcgaagctgtgcagcccgcggtc                      >  GWNJ‑0478:712:GW2002102894th:2:1208:16038:78298/1‑110 (MQ=60)

                                                                           CCTTGCCTTCGAAGCGGCTGTAGAACGCGCCGGTCGTGACGCCGGCCTGCGCGCAGATTTCCTGGATCGAGACCTGTTCCAGCGTGCGCTCGCAGCAGCCGGCGGCCGGCTTCCAGCAGCAGCAGCGTGGTGCGCAGGCCACGCGAATAG                  <  GWNJ‑0478:712:GW2002102894th:2:2215:8283:22754/150‑1 (MQ=60)

                                                                                         CGGCTGTAGAACGCGCCGGTCGTGACGCCGGCCTGCGCGCAGATTTCCTGGATCGAGACCTGTTCCAGCGTGCGCTCGCAGCAGCCGGCGGCCGGCTTCCAGCAGCAGCAGCGTGGTGCGCAGGCCACGCGAATAGCGCGGTGCGATCCT    >  GWNJ‑0478:712:GW2002102894th:2:1212:9152:83411/1‑150 (MQ=60)

                                                                                           GCTGTAGAACGCGCCGGTCGTGACGCCGGCCTGCGCGCAGATTTCCTGGATCGAGACCTGTTCCAGCGTGCGCTCGCAGCAGCCGGCGGCCGGCTTCCAGCAGCtgtctcttatacacatctccgagcccacgagacactcgctaatctc  >  GWNJ‑0478:712:GW2002102894th:2:1209:12795:95115/1‑104 (MQ=60)

                                                                                           GCTGTAGAACGCGCCGGTCGTGACGCCGGCCTGCGCGCAGATTTCCTGGATCGAGACCTGTTCCAGCGTGCGCTCGCAGCAGCCGGCGGCCGGCTTCCAGCAGCAGCAGCGTctgtctcttatacacatctccgagcccacgagacactc  >  GWNJ‑0478:712:GW2002102894th:2:2106:16390:80193/1‑112 (MQ=60)

                                                                                                                       G‑CTGCGCGCAGATTTCCTGGATCGAGACCTGTTCCAGCG                                                                                    <  GWNJ‑0478:712:GW2002102894th:2:2116:17860:34320/39‑1 (MQ=60)

                                                                                                                         CTGCGCGCAGATTTCCTGGATCGAGACCTGTTCC                                                                                        >  GWNJ‑0478:712:GW2002102894th:2:2213:12309:38975/1‑34 (MQ=60)

GTTGCGCAAGCGGCTCGGCCATGCCCTTGCGCAGCGTGGCCAGCACCAGGGCTTGCAGCGCCCTGAAATAGCTATCCTTGCCTTCGAAGCGGCTGTAGAACGCGCCGGTCGTGACGCCGG‑CTGCGCGCAGATTTCCTGGATCGAGACCTGTTCCAGCGTGCGCTCGCAGCAGCCGGCGGCCGGCTTCCAGCAGCAGCAGCGTGGTGCGCAGGCCACGCGAATAGCGCGGTGCGATCCTCG  >  AM260479/275849‑276088

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`