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
A22 F27 I1 R1	17	36.9	1290494	93.0%	1200159	143.6

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	97.9%	143.3 / NA	47	A186E (GCA→GAA)	bglJ	bgl operon transcriptional activator
Reads supporting (aligned to +/- strand): ref base C (1/0); new base A (26/20); total (27/20)
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

GACCGACTGAACAATCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGCACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATCCGCATGATGCCGGGTT  >  NC_000913_3_pae_tpiA/4604490‑4604771

gaccgacTGAACAATCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATaa                                                                                                                                       >  1:301238/1‑149 (MQ=255)

        gAACAATCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCGTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACCCAATATCAAAACGCTCCGTGAAACTAAATTTAAtg                                                                                                                               >  2:364221/1‑149 (MQ=255)

          aCAATCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAAtgtg                                                                                                                             >  1:158406/1‑149 (MQ=255)

             aTCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATg                                                                                                                          <  1:448280/149‑1 (MQ=255)

                  tGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGaa                                                                                                                     >  2:380548/1‑149 (MQ=255)

                    gTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAAc                                                                                                                   >  1:329417/1‑149 (MQ=255)

                      aCATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGTGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTg                                                                                                                 <  1:496587/149‑1 (MQ=255)

                       cATTAACCAAAGCCAGACGTTAAGCCCGACGGAGTGAGAAATATTGCGCTTTATGTCGCGTGGTTACTCAATGACACAAATTGCTGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTgg                                                                                                                <  1:573715/149‑1 (MQ=255)

                         ttAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGGCACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGc                                                                                                              >  1:252570/1‑149 (MQ=255)

                         ttAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGCTGTCGCAACTGGGc                                                                                                              >  2:626211/1‑149 (MQ=255)

                             ccAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCa                                                                                                          >  1:231189/1‑149 (MQ=255)

                              cAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCa                                                                                                          <  1:236668/148‑1 (MQ=255)

                              cAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCa                                                                                                          >  2:236668/1‑148 (MQ=255)

                                 aGCGGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTc                                                                                                      <  1:475088/149‑1 (MQ=255)

                                         gTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGCGCAGCTTAAACGCAATATCAAAACGATCCGTGCACATAAATTTAATGGGATGTCGAAACTGGGCGTAAGTTATGACGCAg                                                                                              >  1:6701/1‑149 (MQ=255)

                                           tAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAggg                                                                                            <  2:413982/149‑1 (MQ=255)

                                              gCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGgttg                                                                                         >  2:261133/1‑149 (MQ=255)

                                                           agaAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAg                                                                            >  2:547483/1‑149 (MQ=255)

                                                                tatTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATAtt                                                                       >  1:459513/1‑149 (MQ=255)

                                                                tatTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGGTCTGACGCAGGGTTGTTGGAGGCCGCAGATAtt                                                                       >  2:128160/1‑149 (MQ=255)

                                                                     cgcTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGAGTTCGTTGCCACTCAGGGTTGTTGGAGGCCGCAGATATTCTGtt                                                                  <  1:155107/149‑1 (MQ=255)

                                                                      tcTTTATGTCGCGAGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTta                                                                 <  1:165160/148‑1 (MQ=255)

                                                                            tGTCGCGTGGCTACTCAATGACCCAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTtatgtatg                                                           >  1:290835/1‑149 (MQ=255)

                                                                             gTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGc                                                          >  1:196856/1‑149 (MQ=255)

                                                                               cgcgTGGCTACTCAAAGACACAAATTGCCGAGTAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTTTTGGAGGCCGCAGATATTCTGTTATGTATGCgg                                                        <  1:60230/149‑1 (MQ=255)

                                                                                  gTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATAGTCTGTTATGTATGCGGCAt                                                     >  1:377381/1‑149 (MQ=255)

                                                                                   tGGCTACTCAATGACATAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCAtt                                                    <  2:446950/149‑1 (MQ=255)

                                                                                     gCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGc                                                  <  1:380548/149‑1 (MQ=255)

                                                                                            aaTGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCTGAACTTGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCCCAGCTATTCTGTTATTTCTGCGGCATTTCGaaaaaa                                           >  2:149438/1‑149 (MQ=255)

                                                                                            aaTGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATCTTATGTTATGTATGCGGCATTGCGAAACaa                                           >  2:576401/1‑149 (MQ=255)

                                                                                            aaTGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACaa                                           >  1:467043/1‑149 (MQ=255)

                                                                                            aaTGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACaa                                           <  1:291036/149‑1 (MQ=255)

                                                                                               tacacAACTGGCCTGGTAGCTTAACCGCAATATCAAAACGATCCGTGAACATACATTCAATGTGATGTCGAAACTGGGCGTCAGTACTGACGAAGGGTTGTTGGAGGCCCCAGATATTCTGTTATGTATGCGGCATCGTAAAACAAGTa                                        <  2:401763/148‑1 (MQ=255)

                                                                                                  gcaAATTGCCGAGCAGCTAAAACGCAATAGCAACACGATACGTGAACATAAATTTACGCTGCTGTCGAAACTGGTCTTCAGTTCTGACGCATGGTGGTTAGAGACCGCAGATATTCTGTTATGTATGCGGCTTTTCGACACAAGTCAtt                                     >  2:288420/2‑148 (MQ=255)

                                                                                                  acaAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAAtg                                     >  1:423022/1‑149 (MQ=255)

                                                                                                  acaAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAAtg                                     >  2:26883/1‑149 (MQ=255)

                                                                                                              acaacTTAAACGCAATATGAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTAGGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCt                         <  2:548632/145‑1 (MQ=255)

                                                                                                                  cTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAACGTGCTGCATCCCTATTa                     >  1:626587/1‑149 (MQ=255)

                                                                                                                  cTTAAACGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTATGTTCGTACGCAGGGGTCGATGAGGCCGCAGATATTCTGTTGTGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTa                     >  1:314785/1‑149 (MQ=255)

                                                                                                                      aaCGCAATATCAAAACGCTCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGTCTCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATcc                 <  1:379249/149‑1 (MQ=255)

                                                                                                                       aCGCAATATCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATCCg                <  2:158406/149‑1 (MQ=255)

                                                                                                                             tatCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTtat                                                                >  1:1953/1‑95 (MQ=255)

                                                                                                                             tatCAAAACGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTtat                                                                <  2:1953/95‑1 (MQ=255)

                                                                                                                                 aaaaCGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTc                                                                      >  2:47546/1‑85 (MQ=255)

                                                                                                                                 aaaaCGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTc                                                                      <  1:47546/85‑1 (MQ=255)

                                                                                                                                   aaCGATCCGTGAACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGATGGAGGCCGCAGATATTCCGTTATGTATGCGGAAATAGTTAGCAAGTAATGTGTTGCATCCCTATTAATCCGCATGATGCCggg    <  1:153211/149‑1 (MQ=255)

                                                                                                                                     cGATCCGTGAATATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATCCGCATGATGCCGGGtt  <  2:377381/149‑1 (MQ=255)

GACCGACTGAACAATCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGCACATAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATCCGCATGATGCCGGGTT  >  NC_000913_3_pae_tpiA/4604490‑4604771

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