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	152	24.9	2083062	91.6%	1908084	109.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	AM260479	3,301,576	+G	intergenic (+45/‑146)	lspA → / → dfp	lipoprotein signal peptidase II/phosphopantothenoylcysteine synthetase/decarboxylase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	AM260479	3,301,574	1	.	G	100.0%	37.7 / NA	11	intergenic (+43/‑148)	lspA/dfp	lipoprotein signal peptidase II/phosphopantothenoylcysteine synthetase/decarboxylase
Reads supporting (aligned to +/- strand): ref base . (0/0); new base G (4/7); total (4/7)

CCGGCCTTCAACGTGGCCGACTGCGCGATCACGGTCGGCGCGGTGCTGCTGATCGTGGACGAGCTGCGCAGGGTGCGGCGCCACTGAGCGCCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCA‑GGTGAGGGGCGGTTCAGCAAGGCACCACGCCACCAGAACCGCCCGCCCTCACCCCCGGCCCCACTCCCGCCGTGCGGGAGTGGGGAGCCAACCCTCAGCCGGCTTCCCCGGTA  >  AM260479/3301445‑3301687

ccggccTTCAACGTGGCCGACTGCGCGATCACGGTCGGCGCGGTGCTGCTGATCGTGGACGAGCTGCGCAGGGTGCGGCGCCACTGAGCGCCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCA‑gggt                                                                                                               <  2:938766/134‑3 (MQ=255)

  ggccTTCAACGTGGCCGACTGCGCGATCACGGTCGGCGCGGTGCTGCTGATCGTGGACGAGCTGCGCAGGGTGCGGCGCCACTGAGCGCCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCA‑gggtga                                                                                                             <  2:648499/134‑5 (MQ=255)

     cTTCAACGTGGCCGACTGCGCGATCACGGTCGGCGCGGTGCTGCTGATCGTGGACGAGCTGCGCAGGGTGCGGCGCCACTGAGCGCCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCAGGGTGAggg                                                                                                           <  1:395045/134‑1 (MQ=255)

                       cgcgATCACGGTCGGCGCGGTGCTGCTGATCGTGGACGAGCTGCGCAGGGTGCGGCGCCACTGAGCGCCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCAGGGTGAGGGGCGGTTCAGCAAGGca                                                                                           <  2:62593/132‑1 (MQ=255)

                                                ctgATCGTGGACGAGCTGCGCAGGGTGCGGCGCCACTGAGCGCCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCAGGGTGAGGGGCGGTTCAGCAAGGCACCACGCCACCAGAACCGCCCGCCCTc                                                                 <  2:549459/133‑1 (MQ=255)

                                                              gCTGCGCAGGGTGCGGCGCCACTGAGCGCCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCAGGGTGAGGGGCGGTTCAGCAAGGCACCACGCCACCAGAACCGCCCGCCCTCACCCCCGGCCCCACt                                                  <  2:674454/134‑1 (MQ=255)

                                                                                     gAGCGCCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCAGGGTGAGGGGCGGTTCAGCAAGGca                                                                                           >  1:159639/1‑70 (MQ=255)

                                                                                     gAGCGCCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCAGGGTGAGGGGCGGTTCAGCAAGGca                                                                                           <  2:159639/70‑1 (MQ=255)

                                                                                                         gCTCTCCCCTCACGGGGAGAGGCCAGGGTGAGGGGCGGTTCAGCAAGGCACCACGCCACCAGAAc                                                                            >  1:403129/1‑65 (MQ=255)

                                                                                                         gCTCTCCCCTCACGGGGAGAGGCCAGGGTGAGGGGCGGTTCAGCAAGGCACCACGCCACCAGAAc                                                                            <  2:403129/65‑1 (MQ=255)

                                                                                                              ccccTCACGGGGAGAGGCCAGGGTGAGGGGCGGTTCAGCAAGGCACCACGCCACCAGAACCGCCCGCCCTCACCCCCGGCCCCACTCCCGCCGTGCGGGAGTGGGGAGCCAACCCTCAGCCGGCTTCCCCGGTa  >  2:565279/1‑134 (MQ=255)

                                                                                                                 cTCACGGGGAGAGGCCAGGGTGAGGGGCGGTTCAGCAAGGCACCACGCCACCAGAAc                                                                            <  1:925509/57‑1 (MQ=255)

                                                                                                                 cTCACGGGGAGAGGCCAGGGTGAGGGGCGGTTCAGCAAGGCACCACGCCACCAGAAc                                                                            >  2:925509/1‑57 (MQ=255)

CCGGCCTTCAACGTGGCCGACTGCGCGATCACGGTCGGCGCGGTGCTGCTGATCGTGGACGAGCTGCGCAGGGTGCGGCGCCACTGAGCGCCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCA‑GGTGAGGGGCGGTTCAGCAAGGCACCACGCCACCAGAACCGCCCGCCCTCACCCCCGGCCCCACTCCCGCCGTGCGGGAGTGGGGAGCCAACCCTCAGCCGGCTTCCCCGGTA  >  AM260479/3301445‑3301687

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

ACCACTGGCCGGCCTTCAACGTGGCCGACTGCGCGATCACGGTCGGCGCGGTGCTGCTGATCGTGGACGAGCTGCGCAGGGTGCGGCGCCACTGAGCGCCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCA‑GGTGAGGGGCGGTTCAGCAAGGCACCACGCCACCAGAACCGCCCGCCCTCACCCCCGGCCCCACTCCCGCCGTGCGGGAGTGGGGAGCCAACCCTCAGCCGGCTTCCCC  >  AM260479/3301437‑3301683

ACCACTGGCCGGCCTTCAACGTGGCCGACTGCGCGATCACGGTCGGCGCGGTGCTGCTGATCGTGGACGAGCTGCGCAGGGTGCGGCGCCACTGAGCGCCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCAGGGTGAGGGG                                                                                                      <  GWNJ‑0478:712:GW2002102894th:2:1213:3454:38821/148‑1 (MQ=60)

            CCTTCAACGTGGCCGACTGCGCGATCACGGTCGGCGCGGTGCTGCTGATCGTGGACGAGCTGCGCAGGGTGCGGCGCCACTGAGCGCCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCA‑GGgtgagggcgggcggttctggtg                                                                                       <  GWNJ‑0478:712:GW2002102894th:2:1209:11675:99655/150‑23 (MQ=60)

                            cctccatgggtaccgtcaatgcatggccctttttttttttcaaacagaagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacaggccagGGTGAGGGGCGGTTCAGCAAGGCACCACGCCACCAGAAC                                                                        <  GWNJ‑0478:712:GW2002102894th:2:1107:18759:14461/39‑1 (MQ=60)

                                           gcagaagacggcatacgagatgtagctccgtctcgtgggctcggagatgtgtataagagacagGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCAGGGTGAGGGGCGGTTCAGCAAGGCACCACGCCACCAGAACCGCCCGCCCTCACCC                                                         <  GWNJ‑0478:712:GW2002102894th:2:2211:2778:63303/87‑1 (MQ=60)

                                                                              GGGTGCGGCGCCACTGAGCGCCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCAGGGTGAGGGGCGGTTCAGCAAGGCACCACGCCACCAGAACCtgtctcttatacacatctccgagcccacgagacggagctacatctcgt                       >  GWNJ‑0478:712:GW2002102894th:2:1110:18055:41385/1‑101 (MQ=60)

                                                                                                  CCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCAGGGTGAGGGGCGGTTCAGCAAGGCACCACGCCACCAGAACCGCCCGCCCTCACCCCtgtctcttatacacatctccgagcccacgagacggagctacatctcgtatgccg  >  GWNJ‑0478:712:GW2002102894th:2:1211:15760:45486/1‑96 (MQ=60)

ACCACTGGCCGGCCTTCAACGTGGCCGACTGCGCGATCACGGTCGGCGCGGTGCTGCTGATCGTGGACGAGCTGCGCAGGGTGCGGCGCCACTGAGCGCCCTGATTGTGTTCCGCTCTCCCCTCACGGGGAGAGGCCA‑GGTGAGGGGCGGTTCAGCAAGGCACCACGCCACCAGAACCGCCCGCCCTCACCCCCGGCCCCACTCCCGCCGTGCGGGAGTGGGGAGCCAACCCTCAGCCGGCTTCCCC  >  AM260479/3301437‑3301683

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: `‑`