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
A3 F2 I1 R1	2892	75.3	5698161	66.1%	3766484	59.5

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	Exported	194,917	G→A	25.0%	intergenic (+113/+87)	nlpE → / ← yaeF	lipoprotein involved with copper homeostasis and adhesion/predicted lipoprotein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	Exported	194,917	0	G	A	25.0%	55.0 / 12.1	28	intergenic (+113/+87)	nlpE/yaeF	lipoprotein involved with copper homeostasis and adhesion/predicted lipoprotein
Reads supporting (aligned to +/- strand): ref base G (6/15); new base A (4/3); total (10/18)
Fisher's exact test for biased strand distribution p-value = 2.07e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.76e-01

TATTTCAACATTTTGAATTTGCACGTTTTTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAATGGTGCTCAAC‑GCCTGATGCGACGCTGGCGCGTCTTATCATGCCTACAACCCCCCTCATACCTTAAGGCG  >  Exported/194849‑194985

tatTTCAACATTTTGAATTTGCACGTTTTTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAATgg                                                                      <  1:407095/70‑1 (MQ=255)

    tCAACATTTTGAATTTGCACGTTTTTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAATgg                                                                      >  1:1185384/1‑66 (MQ=255)

    tCAACATTTTGAATTTGCACGTTTTTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAATgg                                                                      >  1:726452/1‑66 (MQ=255)

     cAACATTTTGAATTTGCACGTTTTTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAATGGTGCTc                                                                 <  1:5423255/70‑1 (MQ=255)

     cAACATTTTGAATTTGCACGTTTTTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAATGGTGCTc                                                                 >  1:634490/1‑70 (MQ=255)

                     cACGTTTTTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAATGGTGCTCAAC‑GCCTGATGCGACg                                                <  1:4878981/70‑1 (MQ=255)

                     cACGTTTTTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAATGGTGCTCAAC‑GCCTGATGCGACg                                                <  1:1848405/70‑1 (MQ=255)

                          tttttGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAATGGTGCTCAAC‑GCCTGATGCGACGCTGgcg                                          >  1:823979/1‑71 (MQ=255)

                          tttttGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAATGGTGCTCAAC‑GCCTGATGCGACGCTGgc                                           >  1:4768027/1‑70 (MQ=255)

                            tccgTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAACAGTGC‑CAACTGCCTGATGCGACGCTCgcgc                                         >  1:3064589/4‑70 (MQ=11)

                             ccgTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAACAGTGC‑CAACTGCCTGATGCGACGCTTGCGCGt                                       >  1:4934577/3‑71 (MQ=11)

                              cgTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAACAGTGC‑CAACTGCCTGATGCGACGCTTGCGCGTc                                      >  1:3941813/2‑71 (MQ=11)

                                tAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAATGGTGCTCAAC‑GCCTGATGCGACGCTGGCGCGTCtt                                    <  1:5137867/71‑1 (MQ=255)

                                tAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAATGGTGCTCAAC‑GCCTGATGCGACGCTGGCGCGTCtt                                    <  1:1143037/71‑1 (MQ=255)

                                  ggCCGGATAAGGCGTTTACGCCGCATCCGGCAACAGTGC‑CAACTGCCTGATGCGACGCTTGCGCGTCTTAt                                  <  1:1916953/71‑1 (MQ=11)

                                   gCCGGATAAGGCGTTTACGCCGCATCCGGCAATGGTGCTCAAC‑GCCTGATGCGACGCTGGCGCGTCTTAt                                  <  1:5507982/70‑1 (MQ=255)

                                   gCCGGATAAGGCGTTTACGCCGCATCCGGCAACAGTGC‑CAACTGCCTGATGCGACGCTTGCGCGTCTTATc                                 <  1:4794087/71‑1 (MQ=11)

                                    ccGTATAAGGCGTTTACGCCGCATCCGGCAACAGTGC‑CAACTGCCTGATGCGACGCTTGCGCGTCTTAt                                  <  1:1212443/69‑1 (MQ=11)

                                       gATAAGGCGTTTACGCCGCATCCGGCAATGGTGCTCAAC‑GCCTGATGCGACGCTGGCGCGTCTTATCATGc                             >  1:883738/1‑71 (MQ=255)

                                             gCGTTTACGCCGCATCCGGCAATGGTGCTCAAC‑GCCTGATGCGACGCTg                                             <  1:957765/49‑1 (MQ=255)

                                             gCGTTTACGCCGCATCCGGCAACAGTGC‑CAACTGCCTGATGCGACGCTTGCGCGTCTTATCAGGCCTACa                        >  1:1408254/1‑70 (MQ=1)

                                               gTTTACGCCGCATCCGGCAATGGTGCCGACT‑GCCTGATGCGACGCTTGCGCGTCTTATCAGGCCTACaaat                     <  1:5002092/71‑3 (MQ=11)

                                                 ttACGCCGCATCCGGCAATGGTGCTCAAC‑GCCTGATGCGACGCTGGCGCGTCTTATCa                                >  1:5319103/1‑58 (MQ=255)

                                                          aTCCGGCAATGGTGCTCAAC‑GCCTGATGCGACGCTGGCGCGTCTTATCATGCCTACAACCCCCCTCATAcc          >  1:4895975/1‑71 (MQ=255)

                                                           tCCGGCAATGGTGCTCAAC‑GCCTGATGCGACGCTGGCGCGTCTTATCATGCCTACAACCCCCCTCATACCt         <  1:5325089/71‑1 (MQ=255)

                                                              ggCAATGGTGCTCAAC‑GCCTGATGCGACGCTGGCGCGTCTTATCATGCCTACAACCCCCCTCATACCTTaa      <  1:3645414/71‑1 (MQ=255)

                                                              ggCAATGGTGCTCAAC‑GCCTGATGCGACGCTGGCGCGTCTTATCATGCCTACAACCCCCCTCATACCTTaa      <  1:3638862/71‑1 (MQ=255)

                                                                  aTGGTGCTCAAC‑GCCTGATGCGACGCTGGCGCGTCTTATCATGCCTACAACCCCCCTCAt             <  1:4844560/60‑1 (MQ=255)

                                                                  aTGGTGCTCAAC‑GCCTGATGCGACGCTGGCGCGTCTTATCATGCCTACAACCCCCCTCAt             <  1:4839344/60‑1 (MQ=255)

                                                                  aTGGTGCTCAAC‑GCCTGATGCGACGCTGGCGCGTCTTATCATGCCTACAACCCCCCTCAt             <  1:103898/60‑1 (MQ=255)

                                                                  aTGGTGCTCAAC‑GCCTGATGCGACGCTGGCGCGTCTTATCATGCCTACAACCCCCCTCATACCTTAAGGCg  <  1:4997723/71‑1 (MQ=255)

TATTTCAACATTTTGAATTTGCACGTTTTTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAATGGTGCTCAAC‑GCCTGATGCGACGCTGGCGCGTCTTATCATGCCTACAACCCCCCTCATACCTTAAGGCG  >  Exported/194849‑194985

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A