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 I205 R1	220	17.5	961422	97.1%	933540	86.5

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	1,854,126	T→C	M121V (ATG→GTG)	ydjK ←	MFS transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,854,126	0	T	C	100.0%	44.4 / NA	14	M121V (ATG→GTG)	ydjK	MFS transporter
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (3/11); total (3/11)

CCACGATTTCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCATCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGG  >  NZ_CP009273/1854050‑1854200

ccACGATTTCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACggcag                                                               <  2:475758/90‑1 (MQ=255)

          tACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGa                                                     <  1:423888/90‑1 (MQ=255)

           aCCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGaa                                                    <  2:101894/90‑1 (MQ=255)

                   tatatTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGa                                                     >  1:218933/1‑81 (MQ=255)

                   tatatTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGa                                                     <  2:218933/81‑1 (MQ=255)

                   tatatTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCatat                                            >  2:18530/1‑90 (MQ=255)

                      atTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCg                                         <  2:400626/90‑1 (MQ=255)

                                  cAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCAc                             <  2:217791/90‑1 (MQ=255)

                                            cGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGC‑GGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATc                  <  2:58346/90‑1 (MQ=255)

                                                    gTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCaa           <  1:247239/90‑1 (MQ=255)

                                                     tAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAat          <  1:256502/90‑1 (MQ=255)

                                                           tCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAAt    >  2:457020/1‑90 (MQ=255)

                                                           tCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGACAAAGCACCGACAACCATCGAGGCAATATGAAt    <  1:384122/90‑1 (MQ=255)

                                                             ccAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATgg  <  2:113490/90‑1 (MQ=255)

CCACGATTTCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCATCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGG  >  NZ_CP009273/1854050‑1854200

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 30 ≤` `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

CGATTTCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCATCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGCCTCATAG  >  NZ_CP009273/1854053‑1854208

CGATTTCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACctgtctcttatacacatc                                                          >  SRR3722087.164204/1‑82 (MQ=60)

      CTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATAT                                                    >  SRR3722087.220874/1‑100 (MQ=60)

       TACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATT                                                   <  SRR3722087.428824/100‑1 (MQ=60)

                                                 GTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGC         <  SRR3722087.249616/100‑1 (MQ=60)

                                                  TAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGCC        <  SRR3722087.258987/100‑1 (MQ=60)

                                                        TCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGACAAAGCACCGACAACCATCGAGGCAATATGAATGGCCTCATAG  <  SRR3722087.388548/100‑1 (MQ=60)

CGATTTCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCATCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGCCTCATAG  >  NZ_CP009273/1854053‑1854208

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 31 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`