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
A21 F36 I1 R1	19	36.4	1272818	94.0%	1196448	142.2

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	97.1%	112.2 / NA	35	A186E (GCA→GAA)	bglJ	bgl operon transcriptional activator
Reads supporting (aligned to +/- strand): ref base C (0/1); new base A (20/14); total (20/15)
Fisher's exact test for biased strand distribution p-value = 4.29e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.93e-01

TGAACAATCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGCACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATCCGCATGATGCCGGGTTTA  >  NC_000913_3_pae_tpiA/4604497‑4604773

tGAACAATCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAAt                                                                                                                                  >  1:615365/1‑149 (MQ=255)

tGAACAATCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAAt                                                                                                                                  >  1:613257/1‑149 (MQ=255)

    cAATCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGa                                                                                                                              <  2:615365/149‑1 (MQ=255)

    cAATCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGa                                                                                                                              <  2:613257/149‑1 (MQ=255)

           tGGTACATTAACCAAAGCCGGAGGTTTTGGCTGATGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTGCTCAATGACACAAATTGTCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGaa                                                                                                                       >  2:584890/1‑149 (MQ=255)

           tGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGaa                                                                                                                       >  2:290236/1‑149 (MQ=255)

               aaaTTAAACAAATCAGGGCGTTGGACACGATGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTg                                                                                                                   <  2:479896/147‑1 (MQ=255)

                 aTTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATGGCCTAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTggg                                                                                                                 <  2:71268/149‑1 (MQ=255)

                     aCCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAAATGGGCGTc                                                                                                             >  1:155047/1‑149 (MQ=255)

                         aaGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGtt                                                                                                         <  1:205381/149‑1 (MQ=255)

                              ggACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATATCGAAACTGGGCGTCAGTTCTGag                                                                                                    >  2:333163/1‑148 (MQ=255)

                                   ttAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAgg                                                                                               <  1:569854/149‑1 (MQ=255)

                                        cccGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGgttgt                                                                                          >  1:113014/1‑149 (MQ=255)

                                            aCGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCTAAACTGGGTGTCAGTTCTGACGCAGGGTTGTTGGa                                                                                      <  2:485425/149‑1 (MQ=255)

                                                    agaAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAGCGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGCCGCAGGGTTGTTGGAGGCCGCAg                                                                              >  2:370864/1‑149 (MQ=255)

                                                     gaAATATTGCGCTTTATGTCGCGTGGCTAATCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGa                                                                             <  1:291397/149‑1 (MQ=255)

                                                                cTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTtat                                                                  >  1:278812/1‑149 (MQ=255)

                                                                cTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATAGTcgggtag                                                                  >  1:277306/1‑143 (MQ=255)

                                                                         gcgTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGc                                                         >  1:112802/1‑149 (MQ=255)

                                                                                  cTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGaaa                                                <  2:514000/149‑1 (MQ=255)

                                                                                   tCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTACGCGGCATTGCGAAAc                                               >  2:330832/1‑149 (MQ=255)

                                                                                             aaaTTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGc                                                            >  1:366585/1‑126 (MQ=255)

                                                                                             aaaTTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGc                                                            <  2:366585/126‑1 (MQ=255)

                                                                                             aaaTTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAAtgtg                                     >  1:132250/1‑149 (MQ=255)

                                                                                               aTTGCCGAGCAGCTTAAACCAAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGtt                                   <  1:615041/149‑1 (MQ=255)

                                                                                                  gCCGAGCAGCTTAAACGCAATATCAAAACGATAAGACCATACAGAATTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCa                                <  1:437485/149‑1 (MQ=255)

                                                                                                        cagcTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTa                          >  2:371645/1‑149 (MQ=255)

                                                                                                                 cGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATCCGc                 >  1:499898/1‑149 (MQ=255)

                                                                                                                     atatCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATCCGCatga             >  1:408626/1‑149 (MQ=255)

                                                                                                                          aaaaCGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATTCCTATTAATCCGCATGATGCCg        >  2:451606/1‑149 (MQ=255)

                                                                                                                          aaaaCGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATCCGCATGCTGCCg        >  1:290748/1‑149 (MQ=255)

                                                                                                                          aaaaCGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATCCGCATGATGCCg        >  1:630893/1‑149 (MQ=255)

                                                                                                                              cGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCTGCATTGCGAAACCAGTAATGTGTTGCATCCCTATTAATCCGCATGATGCCGGGtt    <  2:73416/149‑1 (MQ=255)

                                                                                                                              cGATCCGAGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATCCGCATGATGCCGGGtt    <  2:190104/149‑1 (MQ=255)

                                                                                                                                aTCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATCCGCATGATGCCGGGTTTa  <  1:289994/149‑1 (MQ=255)

TGAACAATCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGCACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATCCGCATGATGCCGGGTTTA  >  NC_000913_3_pae_tpiA/4604497‑4604773

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A