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
A8 F1 I2 R1	97	53.3	2484976	94.5%	2348302	111.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,241,074	C→T	G377G (GGC→GGT)	sstT →	sodium:serine/threonine symporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,241,074	0	C	T	100.0%	123.8 / NA	38	G377G (GGC→GGT)	sstT	sodium:serine/threonine symporter
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (20/18); total (20/18)

CTGTGGCGCATCCGGCGTGGCGGGGGGGTCTCTGCTGCTGATCCCACTGGCCTGTAATATGTTCGGTATTTCGAACGATATCGCCATGCAGGTGGTTGCCGTCGGCTTTATCATCGGCGTATTGCAGGACTCTTGCGAAACCGCGCTGAACTCTTCAACTGACGTGCTGTTCACTGCGGCAGCTTGCCAGGCAGAAGACGATCGTCTGGCAAATAGCGCCCTGCGTAATTAATTGTTTAACC  >  NC_000913/3240957‑3241198

cTGTGGCGCATCCGTCGTGGCGGGGGGGTCTCTGCTGCTGATCCCACTGGCCTGTAATATGTTCGGTATTTCGAACGATATAGCCATGCAGGTGGTTGCGGTCGGCTTTATCATCGGTGTATTGCAGGCCTCTTGCGaa                                                                                                         >  1:752602/1‑139 (MQ=255)

 tgtgGCGCATCCGGCGTGGCGGGGGGGTCTCTGCTGCTGATCCCACTGGCCTGTAATATGTTCGGTATTTCGAACGATATCGCCATGCAGGTGGTTGCCGTCGGCTTTATCATCGGTGTATTGCAGGACTCTTGCGaaa                                                                                                        <  1:432880/139‑1 (MQ=255)

                                            cACTGTCCTGTAATATGTTCGGTATTTCGAACGATATCGCCATGCAGGTGTTTGCCGTCGGCTTTATCATCGGTGTATTg                                                                                                                        <  1:114037/80‑1 (MQ=255)

                                            cACTGGCCTGTAATATGTTCGGTATTTCGAACGATATCGCCATGCAGGTGGTTGCCGTCGGCTTTATCATCGGTGTATTg                                                                                                                        >  2:114037/1‑80 (MQ=255)

                                               tGGCCTGTAATATGTTCGGTATTTCGAACGATATCGCCATGCAGGTGGTTGCCGTCGGCTTTATCATCGGTGTATTGCAGGACTCTTGCGAAACCGCGCTGAACTCTTCAACTGACGTGCTGTTCACTGCGGCAGCTTg                                                          >  1:335494/1‑139 (MQ=255)

                                                           tGTTCGGTATTTCGAACGATATCGCCATGCAGGTGGTTGCCGTCGGCTTTATCATCGGTGTATTGCAGGACTCTTGCGAAACCGCGCTGAACTCTTCAACTGACGTGCTGTTCACTGCGGCAGCTTGCCAGGCagaaga                                              >  2:672021/1‑139 (MQ=255)

                                                           tGTTCGGTATTTCGAACGATATCGCCATGCAGGTGGTTGCCGTCGGCTTTATCATCGGTGTATTGCAGGACTCTTGCGAAACCGCGCTGAACTCTTCAACTGACGTGCTGTTCACTGCGGCAGCTTGCCAGGCagaaga                                              >  1:464885/1‑139 (MQ=255)

                                                           tGTTCGGTATTTCGAACGATATCGCCATGCAGGTGGTTGCCGTCGGCTTTATCATCGGTGTATTGCAGGACTCTTGCGAAACCGCGCTGAACTCTTCAACTGACGTGCTGTTCACTGCGGCAGCTTGCCAGGCagaaga                                              >  1:435045/1‑139 (MQ=255)

                                                           tGTTCGGTATTTCGAACGATATCGCCATGCAGGTGGTTGCCGTCGGCTTTATCATCGGTGTATTGCAGGACTCTTGCGAAACCGCGCTGAACTCTTCAACTGACGTGCTGTTCACTGCGGCAGCTTGCCAGGCagaaga                                              >  1:384332/1‑139 (MQ=255)

                                                              tCGGTATTTCGAACGATATCGCCATGCAGGTGGTTGCCGTCGGCTTTATCATCGGTGTATTGCAGGACTCTTGCGAAACCGCGCTGAACTCTTCAACTGACGTGCTGTTCACTGCGGCAGCTTGCCAgg                                                     >  2:1199572/1‑129 (MQ=255)

                                                              tCGGTATTTCGAACGATATCGCCATGCAGGTGGTTGCCGTCGGCTTTATCATCGGTGTATTGCAGGACTCTTGCGAAACCGCGCTGAACTCTTCAACTGACGTGCTGTTCACTGCGGCAGCTTGCCAgg                                                     <  1:1199572/129‑1 (MQ=255)

                                                                ggTATTTCGAACGATATCGCCATGCAGGTGGTTGCCGTCGGCTTTATCATCGGTGTATTGCAGGAc                                                                                                                  >  1:357172/1‑66 (MQ=255)

                                                                ggTATTTCGAACGATATCGCCATGCAGGTGGTTGCCGTCGGCTTTATCATCGGTGTATTGCAGGAc                                                                                                                  >  1:806883/1‑66 (MQ=255)

                                                                ggTATTTCGAACGATATCGCCATGCAGGTGGTTGCCGTCGGCTTTATCATCGGTGTATTGCAGGAc                                                                                                                  <  2:806883/66‑1 (MQ=255)

                                                                ggTATTTCGAACGATATCGCCATGCAGGTGGTTGCCGTCGGCTTTATCATCGGTGTATTGCAGGAc                                                                                                                  <  2:357172/66‑1 (MQ=255)

                                                                ggTATTTCGAACGATATCGCCATGCAGGTGGTTGCCGTCGGCTTTATCATCGGTGTATTGCAGGACTCTTGCGAAACCGCGCTGAACTCTTCAACTGACGTGCTGTTCACTGCGGCAGCTTGcc                                                        >  1:702589/1‑124 (MQ=255)

                                                                ggTATTTCGAACGATATCGCCATGCAGGTGGTTGCCGTCGGCTTTATCATCGGTGTATTGCAGGACTCTTGCGAAACCGCGCTGAACTCTTCAACTGACGTGCTGTTCACTGCGGCAGCTTGCCAgg                                                     <  2:1208671/127‑1 (MQ=255)

                                                                ggTATTTCGAACGATATCGCCATGCAGGTGGTTGCCGTCGGCTTTATCATCGGTGTATTGCAGGACTCTTGCGAAACCGCGCTGAACTCTTCAACTGACGTGCTGTTCACTGCGGCAGCTTGCCAgg                                                     >  1:1208671/1‑127 (MQ=255)

                                                                ggTATTTCGAACGATATCGCCATGCAGGTGGTTGCCGTCGGCTTTATCATCGGTGTATTGCAGGACTCTTGCGAAACCGCGCTGAACTCTTCAACTGACGTGCTGTTCACTGCGGCAGCTTGCCAGGCAGAAGACGATc                                         >  2:1165748/1‑139 (MQ=255)

                                                                ggTATTTCGAACGATATCGCCATGCAGGTGGTTGCCGTCGGCTTTATCATCGGTGTATTGCAGGACTCTTGCGAAACCGCGCTGAACTCTTCAACTGACGTGCTGTTCACTGCGGCAGCTTGCCAGGCAGAAGACGATc                                         >  2:753600/1‑139 (MQ=255)

                                                                ggTATTTCGAACGATATCGCCATGCAGGTGGTTGCCGTCGGCTTTATCATCGGTGTATTGCAGGACTCTTGCGAAACCGCGCTGAACTCTTCAACTGACGTGCTGTTCACTGCGGCAGCTTGCCAGGCAGAAGACGATc                                         >  1:1120646/1‑139 (MQ=255)

                                                                ggTATTTCGAACGATATCGCCATGCAGGTGGTTGCCGTCAGCTTTATCATCGGTGTATTGCAGGACTCTTGCGAAACCGCTCTGAACTCTTCAACTTACGTGCTGTTCACTGCGGCAGCTTGcc                                                        <  2:702589/124‑1 (MQ=255)

                                                                  tATTTCGATCGATATCGCCATGCAGGTGGTTGCCGTCGGCTTTATCATCGGTGTATTGCAGGACTCTTGCGAAACCGCGCTGAACTCTTCAACTGACGTGCTGTTCACTGCGGCAGCTTGCCAGGCAGAAGACGATCGt                                       <  2:752602/139‑1 (MQ=255)

                                                                       cGAACGATATCGCCATGCAGGTGGTTGCCGTCGGCTTTATCATCGGTGTATTGCAGGACTCTTGCGAAACCGCGCTGAACTCTTCAACTGACGTGCTGTTCACTGCGGCAGCTTGCCAGGCAGAAGACGATCGTCTGGc                                  <  2:986040/139‑1 (MQ=255)

                                                                                             ggtTGCCGTCGGCTTTATCATCGGTGTATTGCAGGACTCTTGCGAAACCGCGCTGAACTCTTCAACTGACGTGCTGTTCACTGCGGCAGCTTGCCAGGCAGAAGACGATCGTCTGGCAAATAGCGCCCTGCGtaattaa            <  2:464885/139‑1 (MQ=255)

                                                                                              gtTGCCGTCGGCTTTATCATCGGTGTATTGCAGGACTCTTGCGAAACCGCGCTGAACTCTTCAACTGACGTGCTg                                                                           <  2:260496/75‑1 (MQ=255)

                                                                                              gtTGCCGTCGGCTTTATCATCGGTGTATTGCAGGACTCTTGCGAAACCGCGCTGAACTCTTCAACTGACGTGCTg                                                                           >  1:260496/1‑75 (MQ=255)

                                                                                              gtTGCCGTCGGCTTTATCATCGGTGTATTGCAGGACTCTTGCGAAACCGCGCTGAACTCTTCAACTGACGTGCTGTTCACTGCGGCAGCTTGCCAGGCAGAAGACGATCGTCTGGCAAATAGCGCCCTGCGtaattaat           <  1:1165748/139‑1 (MQ=255)

                                                                                                tGCCGTCGGCTTTATCATCGGTGTATTGCAGGACTCTTGCGAAACCGCGCTGAACTCTTCAACTGACGTGCTGTTCACTGCGGCAGCTTGCCAGGCAGAAGACGATCGTCTGGCAAATAGCGCCCTGCGTAATTAATTg         >  1:1123905/1‑139 (MQ=255)

                                                                                                 gCCGTCGGCTTTATCATCGGTGTATTGCAGGACTCTTGCGAAACCGCGCTGAACTCTTCAACTGACGTGCTGTTCACTGCGGCAGCTTGCCAGGCAGAAGACGATCGTCTGGCAAAt                              <  2:204230/117‑1 (MQ=255)

                                                                                                 gCCGTCGGCTTTATCATCGGTGTATTGCAGGACTCTTGCGAAACCGCGCTGAACTCTTCAACTGACGTGCTGTTCACTGCGGCAGCTTGCCAGGCAGAAGACGATCGTCTGGCAAAt                              >  1:204230/1‑117 (MQ=255)

                                                                                                   cGTCGGCTTTATCATCGGTGTATTGCAGGACTCTTGCGAAACCGCGCTGAACTCTTCAACTGACGTGCTGTTCACTGCGGCAGCTTGCCAGGCAGAAGACGATCGTCTGGCAAATAGCGCCCTGCGtaattaa            <  2:657225/133‑1 (MQ=255)

                                                                                                   cGTCGGCTTTATCATCGGTGTATTGCAGGACTCTTGCGAAACCGCGCTGAACTCTTCAACTGACGTGCTGTTCACTGCGGCAGCTTGCCAGGCAGAAGACGATCGTCTGGCAAATAGCGCCCTGCGtaattaa            >  1:657225/1‑133 (MQ=255)

                                                                                                     tCGGCTTTATCATCGGTGTATTGCAGGACTCTTGCGAAACCGCGCTGAACTCTTCAACTGACGTGCTGTTCACTGCGGCAGCTTGCCAGGCAGAAGACGATCGTCTGGCAAATAGCGCCCTGCGTAATTAATTGTTTaa    <  2:335494/139‑1 (MQ=255)

                                                                                                     tCGGCTTTATCATCGGTGTATTGCAGGACTCTTGCGAAACCGCGCTGAACTCTTCAACTGACGTGCTGTTCACTGCGGCAGCTTGCCAGGCAGAAGACGATCGTCTGGCAAATAGCGCCCTGCGTAATTAATTGTTTaa    >  1:501959/1‑139 (MQ=255)

                                                                                                      cGGCTTTATCATCGGTGTATTGCAGGACTCTTGCGAAACCGCGCTGAACTCTTCAACTGACGTGCTGTTCACTGCGGCAGCTTGCCAGGCAGAAGACGATCGTCTGGCAAATAGCGCCCTGCGTAATTAATTGTTTAAc   <  1:672021/139‑1 (MQ=255)

                                                                                                       ggCTTTATCATCGGTGTATTGCAGGACTCTTGCGAAACCGCGCTGAACTCTTCAACTGACGTGCTGTTCACTGCGGCAGCTTGCCAGGCAGAAGACGATCGTCTGGCAAATAGCGCCCTGCGTAATTAATTGTTTAAcc  <  1:812046/139‑1 (MQ=255)

                                                                                                                  cGGTGTATTGCAGGACTCTTGCGAAACCGCGCTGAACTCTTCAACTGACGTGCTGTTCACTGCGGCAGCTTGcc                                                        <  2:1146296/74‑1 (MQ=255)

CTGTGGCGCATCCGGCGTGGCGGGGGGGTCTCTGCTGCTGATCCCACTGGCCTGTAATATGTTCGGTATTTCGAACGATATCGCCATGCAGGTGGTTGCCGTCGGCTTTATCATCGGCGTATTGCAGGACTCTTGCGAAACCGCGCTGAACTCTTCAACTGACGTGCTGTTCACTGCGGCAGCTTGCCAGGCAGAAGACGATCGTCTGGCAAATAGCGCCCTGCGTAATTAATTGTTTAACC  >  NC_000913/3240957‑3241198

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 31 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A