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 I228 R1	214	26.5	1448192	97.1%	1406194	86.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	3,113,649	T→G	K330N (AAA→AAC)	glcA ←	glycolate permease GlcA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,113,649	0	T	G	100.0%	90.8 / NA	29	K330N (AAA→AAC)	glcA	glycolate permease GlcA
Reads supporting (aligned to +/- strand): ref base T (0/0); new base G (10/19); total (10/19)

CCGCTTTCAACACTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCTTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGCTCGAATGATTTGCCCCAGAC  >  NZ_CP009273/3113564‑3113731

ccGCTTTCAACACTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTaa                                                                                <  2:510283/90‑1 (MQ=255)

ccGCTTTCAACACTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTaa                                                                                >  2:384016/1‑90 (MQ=255)

       cAACACTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCtt                                                                         >  1:561930/1‑90 (MQ=255)

           acTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATg                                                                     <  2:705087/90‑1 (MQ=255)

           acTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATg                                                                     <  2:644596/90‑1 (MQ=255)

           acTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATg                                                                     <  1:333906/90‑1 (MQ=255)

              tgttgATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTc                                                                  >  1:284011/1‑90 (MQ=255)

               gttgATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTcc                                                                 >  2:213993/1‑90 (MQ=255)

                ttgATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCa                                                                <  2:284011/90‑1 (MQ=255)

                ttgATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCa                                                                <  1:427815/90‑1 (MQ=255)

                    tGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATg                                                            >  1:370614/1‑90 (MQ=255)

                     gCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATgg                                                           <  2:88808/90‑1 (MQ=255)

                     gCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATgg                                                           <  2:152522/90‑1 (MQ=255)

                     gCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATgg                                                           <  1:115233/90‑1 (MQ=255)

                                 tCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCg                                               >  2:603863/1‑90 (MQ=255)

                                     gAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTaa                                           <  2:4852/90‑1 (MQ=255)

                                     gAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTaa                                           <  2:65403/90‑1 (MQ=255)

                                        aTTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGAt                                        >  1:20806/1‑90 (MQ=255)

                                              cACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTaaaaa                                  >  1:99895/1‑90 (MQ=255)

                                                   gTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGGTGGTGACCAGCACCGTTAAGATTAAAAACGGTg                             >  1:123943/1‑90 (MQ=255)

                                                          aaaCGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGc                      >  2:599332/1‑90 (MQ=255)

                                                                    cccGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGCTCGAATGAtt            <  1:174239/90‑1 (MQ=255)

                                                                    cccGGAGCAAATAAAGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGCTCGAATGAtt            <  2:88107/90‑1 (MQ=255)

                                                                     ccGGAGCAAATAACGCGTTAAACGGCTTCAGGGTCCAAAAGGTAACCAGCACCGTTAAGATTAAAAACGGTTACCACGCTCGAATGAttt           <  1:399770/90‑1 (MQ=255)

                                                                         aGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGCTCGAATGATTTGcca       <  2:271890/90‑2 (MQ=255)

                                                                           cAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGCTCGAATGATTTGCCCCa     <  1:603863/90‑1 (MQ=255)

                                                                           cAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGCTCGAATGATTTGCCCCa     <  2:347425/90‑1 (MQ=255)

                                                                              aaaaCGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGCTCGAATGATTTGCCCCAGAc  <  1:104981/88‑1 (MQ=255)

                                                                              aTAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGCTCGAATGATTTGCCCCAGAc  <  2:340628/90‑1 (MQ=255)

CCGCTTTCAACACTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCTTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGCTCGAATGATTTGCCCCAGAC  >  NZ_CP009273/3113564‑3113731

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 24 ≤` `ATCG/ATCG` `< 33 ≤` `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

ATGGGTGCCGCTTTCAACACTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCTTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGCTCGAATGATTTGCCCCAGACTATATTCTGAAGGCA  >  NZ_CP009273/3113557‑3113746

ATGGGTGCCGCTTTCAACACTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACG                                                                                            <  SRR3722112.95813/100‑1 (MQ=60)

    GTGCCGCTTTCAACACTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTT                                                                                        >  SRR3722112.570454/1‑100 (MQ=60)

           TTTCAACACTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTC                                                                                 >  SRR3722112.287304/1‑100 (MQ=60)

                 CACTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATG                                                                           >  SRR3722112.375404/1‑100 (MQ=60)

                  ACTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGG                                                                          <  SRR3722112.337963/100‑1 (MQ=60)

                       TTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACC                                                                     <  SRR3722112.433567/100‑1 (MQ=60)

                            GCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCAC                                                                <  SRR3722112.116666/100‑1 (MQ=60)

                                     GGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGAT                                                       >  SRR3722112.21067/1‑100 (MQ=60)

                                           GGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAA                                                 >  SRR3722112.101141/1‑100 (MQ=60)

                                                TTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGGTGGTGACCAGCACCGTTAAGATTAAAAACGGTG                                            >  SRR3722112.125476/1‑100 (MQ=60)

                                                                           CCCGGAGCAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGCTCGAATGATTTGCCCCAGAC                 <  SRR3722112.176368/100‑1 (MQ=60)

                                                                            CCGGAGCAAATAACGCGTTAAACGGCTTCAGGGTCCAAAAGGTAACCAGCACCGTTAAGATTAAAAACGGTTACCACGCTCGAATGATTTGCCCCACACT                <  SRR3722112.405033/100‑1 (MQ=60)

                                                                                  CAAATAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGCTCGAATGATTTGCCCCAGACTATATTC          <  SRR3722112.613118/100‑1 (MQ=60)

                                                                                     AAAACGCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGCTCGAATGATTTGCCCCAGACTATATTCTGA       <  SRR3722112.106288/100‑1 (MQ=60)

                                                                                          GCGTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGActgtctcttatacacatctgacgctgccgacgaatgtcaatgtgtagatctcgg  >  SRR3722112.51354/1‑46 (MQ=60)

ATGGGTGCCGCTTTCAACACTTGTTGATGCAAATGAGGGATCTGGAAATTAATCACCAGTGAATAAAACGCGCCGCCCGGAGCAAATAACGCTTTAAACGGCTTCATGGTCCAGATGGTGACCAGCACCGTTAAGATTAAAAACGGTGACCACGCTCGAATGATTTGCCCCAGACTATATTCTGAAGGCA  >  NZ_CP009273/3113557‑3113746

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: `‑`