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 I229 R1	214	17.4	943020	97.5%	919444	87.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	3,458,386	A→G	E369G (GAA→GGA)	gspL →	type II secretion system protein GspL

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,458,386	0	A	G	100.0%	75.6 / NA	25	E369G (GAA→GGA)	gspL	type II secretion system protein GspL
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (13/12); total (13/12)

AAAGTCGCTGACCTTAAAAATGAGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGAAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCC  >  NZ_CP009273/3458300‑3458470

aaaGTCGCTGACCTTAAAAATGAGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGgaaa                                                                                   <  1:324733/90‑1 (MQ=255)

 aaGTCGCTGACCTTAAAAATGAGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGgaaaa                                                                                  <  1:449963/90‑1 (MQ=255)

   gTCGCTGACCTTAAAAATGAGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAAc                                                                                <  1:244401/90‑1 (MQ=255)

    tCGCTGACCTTAAAAATGAGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACa                                                                               <  1:197359/90‑1 (MQ=255)

              tAAAAATGAGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATc                                                                     <  1:272083/90‑1 (MQ=255)

                     gAGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAg                                                              >  1:389824/1‑90 (MQ=255)

                     gAGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAg                                                              >  2:203237/1‑90 (MQ=255)

                       gTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAgtg                                                            <  2:389824/90‑1 (MQ=255)

                       gTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAgtg                                                            <  2:344222/90‑1 (MQ=255)

                                 tGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGAc                                                  <  1:6662/90‑1 (MQ=255)

                                 tGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGAc                                                  >  2:2489/1‑90 (MQ=255)

                                 tGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGAc                                                  <  2:218543/90‑1 (MQ=255)

                                  gAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACa                                                 >  1:25213/1‑90 (MQ=255)

                                              gatcgTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATc                                                                     <  1:390762/58‑1 (MQ=255)

                                              gatcgTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATc                                                                     >  2:390762/1‑58 (MQ=255)

                                               atcgTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAg                                    >  1:251907/1‑90 (MQ=255)

                                                tcgTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAgg                                           <  1:345145/82‑1 (MQ=255)

                                                tcgTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAgg                                           >  2:345145/1‑82 (MQ=255)

                                                   tttCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGaa                                <  1:305350/90‑1 (MQ=255)

                                                                  acaGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCAtgg                 <  2:25213/90‑1 (MQ=255)

                                                                     gTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGGTTAAATCAtggtgg              >  2:40034/1‑90 (MQ=255)

                                                                     gTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCAtggtgg              >  1:85052/1‑90 (MQ=255)

                                                                          ggCTTCCGATGGGAAAAACAGTGAAAGATCCGGTCAGTGGTGTATGGAc                                                  >  1:411958/1‑49 (MQ=37)

                                                                          ggCTTCCGATGGGAAAAACAGAGAAAGATCCGGTCAGTGGTGTATGGAc                                                  <  2:411958/49‑1 (MQ=255)

                                                                          ggCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGa         >  2:464575/1‑90 (MQ=255)

                                                                               ccGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAAt    >  2:311836/1‑90 (MQ=255)

                                                                                 gATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATcc  >  1:136401/1‑90 (MQ=255)

AAAGTCGCTGACCTTAAAAATGAGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGAAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCC  >  NZ_CP009273/3458300‑3458470

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 29 ≤` `ATCG/ATCG` `< 34 ≤` `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

AAAGTCGCTGACCTTAAAAATGAGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGAAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAG  >  NZ_CP009273/3458300‑3458485

AAAGTCGCTGACCTTAAAAATGAGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAA                                                                                        <  SRR3722113.327960/100‑1 (MQ=60)

 AAGTCGCTGACCTTAAAAATGAGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAG                                                                                       <  SRR3722113.454721/100‑1 (MQ=60)

   GTCGCTGACCTTAAAAATGAGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGAT                                                                                     <  SRR3722113.246512/100‑1 (MQ=60)

    TCGCTGACCTTAAAAATGAGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATC                                                                                    <  SRR3722113.198890/100‑1 (MQ=60)

           CCTTAAAAATGAGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAG                                                                             >  SRR3722113.393907/1‑100 (MQ=60)

              cggagatgtgtataagagacagAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGG                                                                          <  SRR3722113.394857/78‑1 (MQ=60)

              TAAAAATGAGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGG                                                                          <  SRR3722113.274483/100‑1 (MQ=60)

                        TGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACA                                                                >  SRR3722113.25426/1‑100 (MQ=60)

                                 TGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAAC                                                       <  SRR3722113.6731/100‑1 (MQ=60)

                                     GCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAG                                                   >  SRR3722113.254092/1‑100 (MQ=60)

                                        AATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGA                                                <  SRR3722113.348649/100‑1 (MQ=60)

                                                   TTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAAT                                     <  SRR3722113.308282/100‑1 (MQ=60)

                                                           AGTTAACACAGTCCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGG                             >  SRR3722113.85806/1‑100 (MQ=60)

                                                                ACACAGTCCTGGCTTCCGATGGGAAAAACAGTGAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACctgtctcttatacacatctccgagcccacga                        >  SRR3722113.416305/1‑69 (MQ=60)

                                                                       CCTGGCTTCCGATGGGAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCC                 >  SRR3722113.137544/1‑100 (MQ=60)

                                                                                      GAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAG  <  SRR3722113.55949/100‑1 (MQ=60)

AAAGTCGCTGACCTTAAAAATGAGTGCTAAGAGTGAAGCTAATATCGATCGTTTCTGTGAGTTAACACAGTCCTGGCTTCCGATGGAAAAAACAGAAAAAGATCCGGTCAGTGGTGTATGGACAGTAAGGAACTCAGGGAAATGATTAAATCATGGTGGGCAGAAAAATCCACATCGGAAAAACAG  >  NZ_CP009273/3458300‑3458485

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 30 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`