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 F10 I1 R1	17	30.2	1100966	93.3%	1027201	143.3

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	96.9%	94.6 / NA	32	A186E (GCA→GAA)	bglJ	bgl operon transcriptional activator
Reads supporting (aligned to +/- strand): ref base C (0/1); new base A (15/16); total (15/17)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.98e-01

CCGACTGAACAATCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGCACAT‑AAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATCCGCATGATGCCGGGTT  >  NC_000913_3_pae_tpiA/4604492‑4604771

ccgacTGAACAATCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTAGGTCGCGGGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACAT‑AAAt                                                                                                                                     <  1:57266/149‑1 (MQ=255)

   acTGAACAATCAGTGGTACATTAACCAAAGCCGGACGGTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCACCTTAAACGCAATATCCAACAGATACGTGAAAAT‑AAATTTa                                                                                                                                  >  1:28789/1‑149 (MQ=255)

          aaTCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAGTATCGAATCGATCCGTGAACAT‑AAATTTAATGTGAt                                                                                                                           <  1:408172/149‑1 (MQ=255)

              aGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACAT‑AAATTTAATGTGATGTCg                                                                                                                       >  1:176195/1‑149 (MQ=255)

                     cATTAACCAAAGCCGGACGTTAAGCGCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACAT‑AAATTTAATGTGATGTCGAAACTgg                                                                                                                <  2:281873/149‑1 (MQ=255)

                      aTTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACAT‑AAATTTAATGTGATGTCGaaaatcgg                                                                                                               >  2:439260/1‑144 (MQ=255)

                      aTTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACAT‑AAATTTAATGTGATGTCGAAACTggg                                                                                                               <  2:333928/149‑1 (MQ=255)

                      aTTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACAT‑AAATTTAATGTGATGTCGAAACTggg                                                                                                               <  2:333597/149‑1 (MQ=255)

                              aaGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACAT‑AAATTTAATGTGATGTCGAAACTGGGCGTCAGtt                                                                                                       <  1:146712/149‑1 (MQ=255)

                                gCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACAT‑AAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCt                                                                                                     <  2:176195/149‑1 (MQ=255)

                                      cGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACAT‑AAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCa                                                                                               >  1:6553/1‑149 (MQ=255)

                                          aaGCCCGACGGAGAGAGCAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACAT‑AAATTTAATGTGATGTCCAAACTGGGCGTCAGTTCTGAACCAggtg                                                                                           >  2:300616/1‑147 (MQ=255)

                                                 aCGGAGAGAGAAATTTTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACAT‑AAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGa                                                                                    <  1:50560/149‑1 (MQ=255)

                                                 aCGGAGAGAGAAATTTTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACAT‑AAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGa                                                                                    <  2:178874/149‑1 (MQ=255)

                                                                ttGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACAT‑AAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCt                                                                     >  2:327124/1‑149 (MQ=255)

                                                                    gcTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACAT‑AAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGGAGATATTCTGTta                                                                 >  2:16252/1‑149 (MQ=255)

                                                                    gcTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACAT‑AAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTta                                                                 >  1:324354/1‑149 (MQ=255)

                                                                      tttATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACAT‑AAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTtatg                                                               >  1:248288/1‑149 (MQ=255)

                                                                                    cTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACAT‑AAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCg                                                 <  1:327124/149‑1 (MQ=255)

                                                                                      aCTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGT‑CATATCAGGCTTAAGGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGaa                                               <  1:404029/149‑1 (MQ=255)

                                                                                          aaTGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACAT‑AAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACaa                                           <  2:6553/149‑1 (MQ=255)

                                                                                          aaTGAAACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACAT‑AAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACaa                                           <  1:525955/149‑1 (MQ=255)

                                                                                               cacaAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGAACAT‑AAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAAt                                      >  1:423877/1‑149 (MQ=255)

                                                                                                                 ttAAACGCAATATCAAAACGATCCGTGAACAT‑AAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGa                                                                                    >  2:184757/1‑85 (MQ=255)

                                                                                                                 ttAAACGCAATATCAAAACGATCCGTGAACAT‑AAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGa                                                                                    <  1:184757/85‑1 (MQ=255)

                                                                                                                  tAAACGCAATATCAAAACGATCCGTGAACAT‑AAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATTCTGCATCGCGAAACAACTAATGTCTTGCATCCCTATTAAt                   <  2:248288/149‑1 (MQ=255)

                                                                                                                   aaaCGCAATATCAAAACGATCCGTGAACAT‑AAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCAtt                                                    <  2:151698/115‑1 (MQ=255)

                                                                                                                   aaaCGCAATATCAAAACGATCCGTGAACAT‑AAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCAtt                                                    >  1:151698/1‑115 (MQ=255)

                                                                                                                     aCGCAATATCAAAACGATCCGTGAACAT‑AAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATCCg                >  1:537984/1‑149 (MQ=255)

                                                                                                                           tatCAAAACGATCCGTGAACAT‑AAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGAAGGGGTGTTGGAGGCCGCAGATATTATGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATCCGCatgat          >  2:501498/1‑149 (MQ=255)

                                                                                                                               aaaaCGATCCGTGAACAT‑AAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATCCGCATGATGCCg      >  1:397190/1‑149 (MQ=255)

                                                                                                                                   ctaTCCGTGAACAT‑AAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATACTCTTTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATCCGCATGATGCCGGGtt  <  1:16252/147‑1 (MQ=255)

CCGACTGAACAATCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAACGATCCGTGCACAT‑AAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATCCGCATGATGCCGGGTT  >  NC_000913_3_pae_tpiA/4604492‑4604771

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