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
A23 F79 I1 R1	20	28.5	998386	94.1%	939481	141.6

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	97.3%	118.9 / NA	37	A186E (GCA→GAA)	bglJ	bgl operon transcriptional activator
Reads supporting (aligned to +/- strand): ref base C (1/0); new base A (21/15); total (22/15)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCGACTGAACAATCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGCACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATCCGCATGATGCCGGGTTTACTTC  >  NC_000913_3_pae_tpiA/4604492‑4604777

ccgacTGAACAATCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACAGAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAAt                                                                                                                                           <  2:484936/149‑1 (MQ=255)

ccgacTGAACAATCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAacatacat                                                                                                                                           <  2:339391/149‑1 (MQ=255)

  gacTGAACAATCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGAGGGAGGGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGAGAGAAATTGCAGAGAAGCTTAAACGCAATATCAAAACGATCCGTGCACATCAAttg                                                                                                                                         >  1:394222/1‑148 (MQ=255)

           aTCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATg                                                                                                                                <  1:335195/149‑1 (MQ=255)

            tCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGt                                                                                                                               >  1:241080/1‑149 (MQ=255)

                       ttAACCACAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGc                                                                                                                    <  1:250859/149‑1 (MQ=255)

                       ttAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTAGCATAGATACTTAATTACAAAAATTGCGTAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGc                                                                                                                    >  1:369480/1‑149 (MQ=255)

                                   ggACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAAt                                                                                                                                      <  1:69863/119‑1 (MQ=255)

                                   ggACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAAt                                                                                                                                      >  2:69863/1‑119 (MQ=255)

                                       gTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAg                                                                                                    >  2:61104/1‑149 (MQ=255)

                                        ttAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAgg                                                                                                   <  1:158059/149‑1 (MQ=255)

                                         tAAGCCAGACTGAGTAAGAAATTGTGCGCTGTATGTCGCGTGGCTACTCAATGACACAAATTGCTGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAggg                                                                                                  <  2:193248/149‑1 (MQ=255)

                                           aGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAAAATCAAAACGATCCGGGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGgtt                                                                                                >  2:391576/1‑149 (MQ=255)

                                             cccGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACGCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGGGTCAGTTCTGACGCGGGgttgt                                                                                              >  1:46250/1‑149 (MQ=255)

                                                                           gTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAACATAACAACGCCCCGTGAAAAACAGCTAACTGTGATCCCCAACCAGGCAGCCAGCTGTTACCCATGGGGGTTTGAGGCGGCAGATATTCTGTTATGTATGc                                                                >  2:295847/1‑149 (MQ=255)

                                                                                     tACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGa                                                      >  1:152685/1‑149 (MQ=255)

                                                                                     tACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGa                                                      <  2:15306/149‑1 (MQ=255)

                                                                                       cTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGaaa                                                    >  2:269682/1‑149 (MQ=255)

                                                                                          aaTGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGGGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACaa                                                 <  1:482159/149‑1 (MQ=255)

                                                                                                acaAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGaaa                                                    >  1:65949/1‑140 (MQ=255)

                                                                                                acaAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGaaa                                                    <  2:65949/140‑1 (MQ=255)

                                                                                                    aTTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGtt                                       >  1:198401/1‑149 (MQ=255)

                                                                                                              agcTGAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGTGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTAt                             <  2:241080/149‑1 (MQ=255)

                                                                                                                cTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGGGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTa                           >  2:300298/1‑149 (MQ=255)

                                                                                                                 ttAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTCATGTGTTGCATCCCTATTaa                          >  2:198794/1‑149 (MQ=255)

                                                                                                                 ttAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTaa                          >  2:417602/1‑149 (MQ=255)

                                                                                                                      cGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAACCTGGGGGGCAGTGGTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATCCGc                     <  1:367176/149‑1 (MQ=255)

                                                                                                                           tatCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTACATCCTTATTAATCCGCctgat                >  2:200043/1‑149 (MQ=255)

                                                                                                                             tCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATCCGCCTGATGc              >  1:160263/1‑149 (MQ=255)

                                                                                                                                    gATCCGTGAACATAAATTTAATGTGATGTCGCAAAAATGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATCCGCATGATGCCGGGttt       >  1:248395/1‑149 (MQ=255)

                                                                                                                                     aTCCGTGAACATAAATTTAATGTGATGACGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTAGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTAGTAATCCGCATGATGCCGGGTTTa      >  1:421528/1‑149 (MQ=255)

                                                                                                                                      tCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATCCGCATGATGCCGGGTTTAc     <  2:248395/149‑1 (MQ=255)

                                                                                                                                      tCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATCCGCATGATGCCGGGTTTAc     <  1:49157/149‑1 (MQ=255)

                                                                                                                                         gTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTa                                              <  1:90691/105‑1 (MQ=255)

                                                                                                                                         gTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTa                                              >  2:90691/1‑105 (MQ=255)

                                                                                                                                         gTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATCCGCATGATGCCGGGTTTACTTc  >  2:196778/1‑149 (MQ=255)

                                                                                                                                         gTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGATTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATCACGCAACCACTACTCTCTTGCAGCCCTATTAATCCGCATGATGCCGGGTTTACTTc  >  2:52946/1‑149 (MQ=255)

CCGACTGAACAATCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGCACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATCCGCATGATGCCGGGTTTACTTC  >  NC_000913_3_pae_tpiA/4604492‑4604777

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A