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
A13 F191 I1 R2	32	34.5	741600	95.9%	711194	140.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP000730	2,026,655	C→T	E87K (GAA→AAA)	vraR ←	response regulator VraR

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	2,026,655	0	C	T	94.7%	53.5 / ‑3.3	19	E87K (GAA→AAA)	vraR	response regulator VraR
Reads supporting (aligned to +/- strand): ref base C (0/1); new base T (8/10); total (8/11)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.11e-01

TAAAACTTCCGGTTCAAAAACAGATTCTCCTCTAGAAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATCCATAAGTAAATCCATTAAAATTAAATCTGGCTTCAACTCATGGGCTTT  >  CP000730/2026521‑2026787

tAAGACTTCCGGTTCAAAAACAGATTCGCCTCTAGAAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTCATGCACGATATACCTCTTTATCTTTAATaaa                                                                                                                                <  2:101453/141‑1 (MQ=255)

tAAAACTTCCGGTTCAAAAACAGATTCTCCTCTAGAAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTTAATaaa                                                                                                                                <  2:101429/141‑1 (MQ=255)

                        ttCTCCTCTAGAAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAAt                                                                                                        <  2:295544/141‑1 (MQ=255)

                                tAGAAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTa                                                                                                >  2:132985/1‑141 (MQ=255)

                                     gTTTTACGAACTGCATCGGCGATATCTATTGCACTTGTTGTTTTTAAAATGTAACTGTCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACACTAATACTTTAATTTGCGGTAAATCt                                                                                           >  2:362262/1‑141 (MQ=255)

                                      ttttACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCtt                                                                                          <  2:236099/141‑1 (MQ=255)

                                             aaCTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAAt                                                                                   >  1:31071/1‑141 (MQ=255)

                                                   aTCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAgt                                                                             <  2:122044/141‑1 (MQ=255)

                                                    tCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAgtc                                                                            <  2:193515/141‑1 (MQ=255)

                                                       gCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAgtcgtc                                                                         <  1:364495/141‑1 (MQ=255)

                                                                              ttttAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATc                                                  >  1:63651/1‑141 (MQ=255)

                                                                                        tctttATCGACACCTGCATCTAATGCACGATATCCCTCTTTATCTTTAATAAAACTAGTTGACATTAATACTTTAATTTGTGTTAAATCTTTTTTAATCTGAGACGTCGCTTCTACACCATCCATGTCATCCATAACTaaa                                        >  2:304691/5‑141 (MQ=255)

                                                                                                  cacCTGCATCTAATGCACGATATACATCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATCCATAAGTAAATCCattaaaa                              >  2:236125/1‑141 (MQ=255)

                                                                                                       gCATCTAATGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTCAATCTGAgtcgt                                                                          <  1:238682/92‑1 (MQ=255)

                                                                                                       gCATCTAATGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTCAATCTGAgtcgt                                                                          >  2:238682/1‑92 (MQ=255)

                                                                                                        cATCTAATGCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATCCATAAGTAAATCCATTAAAATTAAAt                        <  1:368047/141‑1 (MQ=255)

                                                                                                                gCACGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATCCATAAGTAAATCCATTAAAATTAAATCTGGCTTc                >  1:193943/1‑141 (MQ=255)

                                                                                                                   cGATATACCTCTTTATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATCCATAAGTAAATCCATTAAAATTAAATCTGGCTTCAAc             <  2:352227/141‑1 (MQ=255)

                                                                                                                            tctttatctttaATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATCCATAAGTAAATCCATTAAAATTAAATCTGGCTTCAACTCATGGGCt    <  1:237878/141‑1 (MQ=255)

                                                                                                                              tttATCTTTAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATCCATAAGTAAATCCATTAAAATTAAATCTGGCTTCAACTCATGGGCttt  <  2:48200/141‑1 (MQ=255)

TAAAACTTCCGGTTCAAAAACAGATTCTCCTCTAGAAGTTTTACGAACTGCATCGGCGATATCTTTTGCACTTGTTGTTTTTAAAATGTAACTATCGACACCTGCATCTAATGCACGATATACCTCTTTATCTTCAATAAAACTAGTTAACATTAATACTTTAATTTGCGGTAAATCTTTTTTAATCTGAGTCGTCGCTTCTACACCATCCATGTCATCCATAAGTAAATCCATTAAAATTAAATCTGGCTTCAACTCATGGGCTTT  >  CP000730/2026521‑2026787

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A