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
A15 F8 I1 R1	16	40.3	1420662	94.4%	1341104	140.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913_3_pae_tpiA	4,604,632	C→A	A186E (GCA→GAA)	bglJ →	bgl operon transcriptional activator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913_3_pae_tpiA	4,604,632	0	C	A	97.0%	100.1 / ‑3.6	33	coding (557/678 nt)	bglJ	bgl operon transcriptional activator
Reads supporting (aligned to +/- strand): ref base C (0/0); major base A (16/16); minor base . (0/1); total (16/17)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.92e-01

ACCGACTGAACAATCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGCACATAAATTTA‑ATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATCCGCATGATGCCGG  >  NC_000913_3_pae_tpiA/4604491‑4604768

accgacTGAACAATCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGTCTACTCAATTACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATaaa                                                                                                                                    >  1:325134/1‑149 (MQ=255)

    acTGAACAATCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTCCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTa                                                                                                                                >  1:196622/1‑149 (MQ=255)

                        ttAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTA‑ATGTGCTGTCGAAACTGAGc                                                                                                           >  2:318175/1‑149 (MQ=255)

                        ttAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTA‑ATGTGATGTCGAAACTGGGc                                                                                                           <  2:134590/149‑1 (MQ=255)

                        ttAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTA‑ATGTGATGTCGAAAATGGGc                                                                                                           >  2:253604/1‑149 (MQ=255)

                           aCCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCATTACGACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATAACAAAACGATCCGTAAACATAAATTTA‑ATGTGAAGTCGAAACTGGGCGTc                                                                                                        >  1:560735/1‑149 (MQ=255)

                                 gCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTA‑ATGTGATGTCGAAACTGGGCGTCAGTTCt                                                                                                  <  1:613539/149‑1 (MQ=255)

                                   cGGAAGTTAATGCCGACGTAGAGAGAAATATTGTGTTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTA‑ATGTGATGTCGAAACTGGGCGTCAGTTCTGa                                                                                                <  2:416208/149‑1 (MQ=255)

                                              ccgggcGGAGAGAGAAATATTGCGCTTGATGTCGGGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATATATTTA‑ATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGgttgt                                                                                     <  2:414078/144‑1 (MQ=255)

                                                          agaAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAACCGCAATATCAAAACGATCCGTGAACATAAATTTA‑ATGTGATGTCGAAACTGGGGGTCAGTTTTAACACAGGGTTGTTGGAGGCCGCAg                                                                         >  1:595819/1‑149 (MQ=255)

                                                                 ttGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTA‑ATGTGATGTCGAAACTGGGc                                                                                                           >  2:575706/1‑108 (MQ=255)

                                                                 ttGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTA‑ATGTGATGTCGAAACTGGGc                                                                                                           <  1:575706/108‑1 (MQ=255)

                                                                 ttGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTA‑ATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCt                                                                  >  2:665737/1‑149 (MQ=255)

                                                                            gTCGCGTGGCTACTCAATGACACGAATTGCCGAGCAGCTTAAGCGAAATATCAAAACGATCCGTGAACATAAATTTA‑ATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAAGGTTGTTGGAGGCCGCAGATATTCTGTtatgtatga                                                       >  1:565485/1‑148 (MQ=255)

                                                                               gcgTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAGACGGAATCCATAGACTGTACGTGAATAGAGATTTA‑ATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCAGCAGATTTTCTGTTATGTATGCgtc                                                    >  1:699324/1‑147 (MQ=255)

                                                                                        cTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTA‑ATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGaaa                                           <  2:500830/149‑1 (MQ=255)

                                                                                           aaTGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTA‑ATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACaa                                        >  1:435075/1‑149 (MQ=255)

                                                                                                cacaAATTGCCGAGCAGCTTAACAGCAATTTCTTAACGATCCGTGAACATAAATTTA‑ATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTGTGCGGCATTGCGAAACAAGTAAt                                   >  2:156400/1‑149 (MQ=255)

                                                                                                cacaAATTGCCGAGCAGCGTAAACGCAATATCAAAACGATCCGTGAACATAAATTTA‑ATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAAt                                   <  1:340819/149‑1 (MQ=255)

                                                                                                 acaAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTA‑ATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAAtg                                  >  2:275011/1‑149 (MQ=255)

                                                                                                 acaAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTG‑AAACCAATAGATATTGCATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAAtg                                  <  1:318175/149‑1 (MQ=255)

                                                                                                     aTTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTA‑ATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGtt                              <  1:665737/149‑1 (MQ=255)

                                                                                                     aTTGCCGAGCAGCTGACACGGCATATCAAATCGATACGTCAACTTAAATTAA‑ATGTTCGCTCGAAATATGGAGTCAGTCTTGACGCATGGTTGTGGGAAGCCGCAGATATGCTGTTATGTACGCGGCATTGCGAAACAAGTAATGTGtt                              <  2:699324/149‑1 (MQ=255)

                                                                                                           tgccagcTTAAACTTAATATCAAAACCATCCTTGAACATAAATTTA‑ATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATcc                        <  1:249471/146‑1 (MQ=255)

                                                                                                             gaagcTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTA‑ATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCt                      <  2:390974/147‑1 (MQ=255)

                                                                                                               agcTTAAACGCAATATTAAAACGATCCGTGAACATAAATTTA‑ATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTAt                    <  2:196622/149‑1 (MQ=255)

                                                                                                                       cGCAATATCAAAACGATCCGTGAACATAAATTTA‑ATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGTAACAAGTATGGTGTTGCATCCCTCTTAATCCGc            >  1:181559/1‑149 (MQ=255)

                                                                                                                       cGCAATATCAAAACGATCCGTGAACATAAATTTA‑ATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATccc                       <  1:464814/138‑1 (MQ=255)

                                                                                                                       cGCAATATCAAAACGATCCGTGAACATAAATTTA‑ATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATccc                       >  2:464814/1‑138 (MQ=255)

                                                                                                                         cAATATCAAAACAGACCGGTAATATAAATTTA‑ATTTGATGTCGAAACTGGGCATCAGTTCTGACTCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATCCGCat          <  2:462310/149‑1 (MQ=255)

                                                                                                                            tatCAAAACGATCCGTGAACATAAATTTA‑ATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTgg                                                                                  >  1:447893/1‑74 (MQ=255)

                                                                                                                            tatCAAAACGATCCGTGAACATAAATTTA‑ATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTgg                                                                                  <  2:447893/74‑1 (MQ=255)

                                                                                                                                 aaaCTATCCGTGAACTTAAATTTA‑ATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGTGAAACAAGTAATGTGTTGCATCCCTATTAATCCGCATGATGCCgg  <  1:564241/149‑1 (MQ=255)

ACCGACTGAACAATCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGCACATAAATTTA‑ATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATCCGCATGATGCCGG  >  NC_000913_3_pae_tpiA/4604491‑4604768

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A