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 F1 I1 R1	154	26.6	2069536	90.2%	1866721	108.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	AM260479	2,787,923	+C	intergenic (+165/‑55)	cafA2 → / → moaA1	Ribonuclease G and E/molybdopterin biosynthesis protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	AM260479	2,787,920	1	.	C	100.0%	49.5 / NA	14	intergenic (+162/‑58)	cafA2/moaA1	Ribonuclease G and E/molybdopterin biosynthesis protein
Reads supporting (aligned to +/- strand): ref base . (0/0); new base C (8/6); total (8/6)

GTCTCCTTTTTTCATGGGCAGCCGGCCGGATGAATCCCCGCCATCTCCGGGGGATGCGGGTGCCCCACCCCCGCCTCGGCTAGAATGGCAGCAGAAGGCATCCGGCCCTCGAGCG‑CCCTGATTTGGCCACGCCGCCAGGCCGCTCCCCGGACGCCGTGCCCACCCACAGGCCATGACCGAATCCGTCATTCC  >  AM260479/2787806‑2787997

gTCTCCTTTTTTCATGGGCAGCCGGCCGGATGAATCCCCGCCATCTCCGGGGGATGCGGGTGCCCCACCCCCGCCTCGGCTAGAATGGCAGCAGAAGGCATCCGGCCCTCGATCGCCCCTGATTTGGCCAcgcc                                                             >  1:288161/1‑134 (MQ=255)

      ttttttCATGGGCAGCCGGCCGGATGAATCCCCGCCATCTCCGGGGGATGCGGGTGCCCCACCCCCGCCTCGGCTAGAATGGCAGCAGAAGGCATCCGGCCCTCGAGCGCCCCTGATTTGGCCAc                                                                >  1:441700/1‑125 (MQ=255)

      ttttttCATGGGCAGCCGGCCGGATGAATCCCCGCCATCTCCGGGGGATGCGGGTGCCCCACCCCCGCCTCGGCTAGAATGGCAGCAGAAGGCATCCGGCCCTCGAGCGCCCCTGATTTGGCCAc                                                                <  2:441700/125‑1 (MQ=255)

      ttttttCATGGGCAGCCGGCCGGATGAATCCCCGCCATCTCCGGGGGATGCGGGTGCCCCACCCCCGCCTCGGCTAGAATGGCAGCAGAAGGCATCCGGCCCTCGAGCGCCCCTGATTTGGCCACGCCGCCAgg                                                       >  2:814223/1‑134 (MQ=255)

                       ggccggATGAATCCCCGCCATCTCCGGGGGATGCGGGTGCCCCACCCCCGCCTCGGCTAGAATGGCAGCAGAAGGCATCCGGCCCTCGAGCGCCCCTGATTTGGCCACGCCGCCAGGCCGCTCCCCGGACGCCg                                      <  1:814223/134‑1 (MQ=255)

                        gccggATGAATCCCCGCCATCTCCGGGGGATGCGGGTGCCCCACCCCCGCCTCGGCTAGAATGGCAGCAGAAGGCATCCGGCCCTCGAGCGCCCCTGATTTGGCCACGCCGCCAg                                                        <  1:1006794/115‑1 (MQ=255)

                        gccggATGAATCCCCGCCATCTCCGGGGGATGCGGGTGCCCCACCCCCGCCTCGGCTAGAATGGCAGCAGAAGGCATCCGGCCCTCGAGCGCCCCTGATTTGGCCACGCCGCCAg                                                        >  2:1006794/1‑115 (MQ=255)

                                                gggggATGCGGGTGCCCCACCCCCGCCTCGGCTAGAATGGCAGCAGAAGGCATCCGGCCCTCGAGCGCCCCTGAtt                                                                       >  1:329092/1‑76 (MQ=255)

                                                gggggATGCGGGTGCCCCACCCCCGCCTCGGCTAGAATGGCAGCAGAAGGCATCCGGCCCTCGAGCGCCCCTGAtt                                                                       <  2:329092/76‑1 (MQ=255)

                                                gggggATGCGGGTGCCCCACCCCCGCCTCGGCTAGAATGGCAGCAGAAGGCATCCGGCCCTCGAGCGCCCCTGATTTGGCCACGCCGCCAGGCCGCTCCCCg                                             >  1:460982/1‑102 (MQ=255)

                                                gggggATGCGGGTGCCCCACCCCCGCCTCGGCTAGAATGGCAGCAGAAGGCATCCGGCCCTCGAGCGCCCCTGATTTGGCCACGCCGCCAGGCCGCTCCCCg                                             <  2:460982/102‑1 (MQ=255)

                                                           gTGCCCCACCCCCGCCTCGGCTAGAATGGCAGCAGAAGGCATCCGGCCCTCGAGCGCCCCTGATTTGGCCACGCCGCCAGGCCGCTCCCCGGACGCCGTGCCCACCCACAGGCCATGACCGAATCCGTCATTcc  >  2:938279/1‑134 (MQ=255)

                                                                                       gcagcaGAAGGCATCCGGCCCTCGAGCGCCCCTGATTTGGCCACGCCGCCAGGCCGCTCCCCGGACGCCGt                                     <  1:414506/71‑1 (MQ=255)

                                                                                       gcagcaGAAGGCATCCGGCCCTCGAGCGCCCCTGATTTGGCCACGCCGCCAGGCCGCTCCCCGGACGCCGt                                     >  2:414506/1‑71 (MQ=255)

GTCTCCTTTTTTCATGGGCAGCCGGCCGGATGAATCCCCGCCATCTCCGGGGGATGCGGGTGCCCCACCCCCGCCTCGGCTAGAATGGCAGCAGAAGGCATCCGGCCCTCGAGCG‑CCCTGATTTGGCCACGCCGCCAGGCCGCTCCCCGGACGCCGTGCCCACCCACAGGCCATGACCGAATCCGTCATTCC  >  AM260479/2787806‑2787997

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

CAAAGCAAGAAGGGGACGGCCACGCCGTCTCCTTTTTTCATGGGCAGCCGGCCGGATGAATCCCCGCCATCTCCGGGGGATGCGGGTGCCCCACCCCCGCCTCGGCTAGAATGGCAGCAGAAGGCATCCGGCCCTCGAGCG‑CCCTGATTTGGCCACGCCGCCAGGCCGCTCCCCGGACGCCGTGCCCACCCACAGGCCATGACCGAATCCGTCATTCCGATTTTCGACCTGCGCGACCATCGCTACCGCTCGATGACGCCCAGCATTCCCGGCAAGCTGGCTGCCCCCAC  >  AM260479/2787780‑2788069

CAAAGCAAGAAGGGGACGGCCACGCCGTCTCCTTTTTTCATGGGCAGCCGGCCGGATGAATCCCCGCCATCTCCGGGGGATGCGGGTGCCCCACCCCCGCCTCGGCTAGAATGGCAGCAGAAGGCATCCGGCCCTCGAGCGCCCCTGATT                                                                                                                                               <  GWNJ‑0478:712:GW2002102894th:2:1107:11523:64707/150‑1 (MQ=60)

      ttcttttgtttttttttttttcaagcagaagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacagCCCCCGCCTCGGCTAGAATGGCAGCAGAAGGCATCCGGCCCTCGAGCGCCCCTGATTTGGCC                                                                                                                                          <  GWNJ‑0478:712:GW2002102894th:2:1111:4356:71086/62‑1 (MQ=60)

           GGGGACGGCCACGCCGTCTCCTTTTTTCATGGGCAGCCGGCCGGATGAATCCCCGCCATCTCCGGGGGATGCGGGTGCCCCACCCCCGCCTCGGCTAGAATGGCAGCAGAAGGCATCCGGCCCTCGATCGCCCCTGATTTGGCCACGCCG                                                                                                                                    >  GWNJ‑0478:712:GW2002102894th:2:1202:14403:34684/1‑150 (MQ=60)

                 GGCCACGCCGTCTCCTTTTTTCATGGGCAGCCGGCCGGATGAATCCCCGCCATCTCCGGGGGATGCGGGTGCCCCACCCCCGCCTCGGCTAGAATGGCAGCAGAAGGCATCCGGCCCTCGAGCGCCCCTGATTTGGCCACGCCGCCAGGC                                                                                                                              >  GWNJ‑0478:712:GW2002102894th:2:1213:20934:77814/1‑150 (MQ=60)

                              gacagTTTCATGGGCAGCCGGCCGGATGAATCCCCGCCATCTCCGGGGGATGCGGGTGCCCCACCCCCGCCTCGGCTAGAATGGCAGCAGAAGGCATCCGGCCCTCGAGCGCCCCTGATTTGGCCACGCCGCCAGGCCGCTCCCCGGACG                                                                                                                 <  GWNJ‑0478:712:GW2002102894th:2:2215:18995:47060/145‑1 (MQ=60)

                                                CGGCCGGATGAATCCCCGCCATCTCCGGGGGATGCGGGTGCCCCACCCCCGCCTCGGCTAGAATGGCAGCAGAAGGCATCCGGCCCTCGAGCGCCCCTGATTTGGCCACGCCGCCAGGCCGCTCCCCGGACGCCGTGCCCACCCACAGGC                                                                                               <  GWNJ‑0478:712:GW2002102894th:2:2202:18310:85414/150‑1 (MQ=60)

                                                 acgagatgtagctccgtctcgtgggctcggagatgtgtataagagacagGCCTCGGCTAGAATGGCAGCAGAAGGCATCCGGCCCTCGAGCGCCCCTGATTTGGCCACGCCGCCAGGCCGCTCCCCGGACGCCGTGCCCACCCACAGGCC                                                                                              <  GWNJ‑0478:712:GW2002102894th:2:1210:16812:24919/101‑1 (MQ=60)

                                                           ATCCCCGCCATCTCCGGGGGATGCGGGTGCCCCACCCCCGCCTCGGCTAGAATGGCAGCAGAAGGCATCCGGCCCTCGAGCGCCCCTGATTTGGCCACGCCGCCAGctgtctcttatacacatctccgagcccacgagacggagctacat                                                                                    >  GWNJ‑0478:712:GW2002102894th:2:1207:18772:7280/1‑106 (MQ=60)

                                                           ATCCCCGCCATCTCCGGGGGATGCGGGTGCCCCACCCCCGCCTCGGCTAGAATGGCAGCAGAAGGCATCCGGCCCTCGAGCGCCCCTGATTTGGCCACGCCGCCAGGCCGCTCCCCGGACGCCGTGCCCACCCtgtctcttatacacatc                                                                                    >  GWNJ‑0478:712:GW2002102894th:2:1212:15472:86837/1‑133 (MQ=60)

                                                                                               agatgtagctccgtctcgtgggctcggagatgtgtataagagacagcCCCTGATTTGGCCACGCCGCCAGGCCGCTCCCCGGACGCCGTGCCCACCCACAGGCCATGACCGAATCCGTCATTCCGATTTTCGACCTGCGCGACCATCGCT                                                <  GWNJ‑0478:712:GW2002102894th:2:1108:20722:45238/103‑1 (MQ=60)

                                                                                                                                            C‑CCCTGATTTGGCCACGCCGCCAGGCCGCTCCCCGGACGCCGTGCCCACCCACAGGCCATGACCGAATCCGTCATTCCGATTTTCGACCctgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccgtcttct  >  GWNJ‑0478:712:GW2002102894th:2:2208:11412:100855/1‑89 (MQ=60)

                                                                                                                                            C‑CCCTGATTTGGCCACGCCGCCAGGCCGCTCCCCGGACGCCGTGCCCACCCACAGGCCATGACCGAATCCGTCATTCCGATTTTCGACCTGCGCGACCATCGCTACCGCTCGATGACGCCCAGCATTCCCGGCAAGCTGGCTGCCCCCAC  >  GWNJ‑0478:712:GW2002102894th:2:1111:20076:75898/1‑150 (MQ=60)

CAAAGCAAGAAGGGGACGGCCACGCCGTCTCCTTTTTTCATGGGCAGCCGGCCGGATGAATCCCCGCCATCTCCGGGGGATGCGGGTGCCCCACCCCCGCCTCGGCTAGAATGGCAGCAGAAGGCATCCGGCCCTCGAGCG‑CCCTGATTTGGCCACGCCGCCAGGCCGCTCCCCGGACGCCGTGCCCACCCACAGGCCATGACCGAATCCGTCATTCCGATTTTCGACCTGCGCGACCATCGCTACCGCTCGATGACGCCCAGCATTCCCGGCAAGCTGGCTGCCCCCAC  >  AM260479/2787780‑2788069

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`