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	4,158,704	C→T	T100I (ACA→ATA)	oxyR →	oxidative and nitrosative stress transcriptional regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913_3_pae_tpiA	4,158,704	0	C	T	100.0%	92.0 / NA	29	T100I (ACA→ATA)	oxyR	oxidative and nitrosative stress transcriptional regulator
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (16/13); total (16/13)

GCCGTAAAGTGTTGTTCACCCAGGCGGGAATGCTGCTGGTGGATCAGGCGCGTACCGTGCTGCGTGAGGTGAAAGTCCTTAAAGAGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCCCACAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGACCTTTCCAAAGCTGGAAATGTATCTGCATGAAGCACAGACCCACCAGTTACTGGCGCAACTGGACAGCGGCAAACTCGATTGCGTGATCCTCGCG  >  NC_000913_3_pae_tpiA/4158560‑4158846

ggcGTAAAGCGTTGTTCACCCAGGCGGGAATGCTGCTGGTGGATCAGGCGCGTACCGTGCTGCGTGAGGTGAAAGGCCTTAAAGTGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCCCATAGtt                                                                                                                                            <  2:309539/147‑1 (MQ=255)

gctctcaaGTGCTGTTCAACCAGGTGGAAATGCTGGTGGTGTATCAGGCGCGTACCTTCCTGCGTGAGGTGAAAGTCCTTAAAGAGATGGCAAGCCAGCAGCCCGAGACGATGTCCGGACCGTTGCACATTTGTTTGATTCCCATAGtt                                                                                                                                            <  2:63065/143‑1 (MQ=255)

                cACCCAGGCGGGAATGCTGCTGGTGGATCAGGCGCGTACCGTGCTGCGTGAGGTGAAAGTCCTTAAAGAGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCCCATAGTTGGACCGTACCTGCTAc                                                                                                                            <  1:425579/149‑1 (MQ=255)

                 aCCCAGGCGGGAATGCTGCTGGTGGATCAGGCGCGTACCGTGCTGCGTGAGGTGAAAGTCCTTAAAGAGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCCCATAGTTGGACCGTACCTGCTaac                                                                                                                           >  1:142623/1‑147 (MQ=255)

                       gCGGGAATGCTGCTGGCTGAGCAGGCGCGTACCGTGCTGCGTCAGGCGAAAGTCCTTAAAGAGATGGCAAGCCAGCATGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCCCATAGTTGGACCGTACCTGCTACCGCatat                                                                                                                     <  2:135971/149‑1 (MQ=255)

                        cGGGAATGCTGCTGGTGGATCAGGCGCGTACCGTGCTGCGTGAGGTGAAAGTCCTTAAAGAGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCCCATAGTTGGACCGTACCTGCTACCGCAtatt                                                                                                                    >  2:335437/1‑149 (MQ=255)

                            aaTGCTGCTGGTGGATCAGGCGCGTACCGTGCTGCGTGAGGTGAAAGTCCGTAAAGAGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCCCATAGTTGGACCGTACCTGCTACCGCATATTATcc                                                                                                                >  2:244621/1‑149 (MQ=255)

                                           tCAGGCGCGTACCGTGCTGCGTGAGGTGAAAGTCCTTAAAGAGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCCCATAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGa                                                                                                 >  1:299007/1‑149 (MQ=255)

                                             aGGCGCGTACCGTGCTGCGTGAGGTGAAAGTCCTTAAAGAGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCCCATAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGAcc                                                                                               >  2:178845/1‑149 (MQ=255)

                                                     aCCGTGCTGCGTGAGGTGAAAGTCCTTAAAGAGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCCCATAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGACCTTTCCaaa                                                                                       >  2:395453/1‑149 (MQ=255)

                                                         tgctgcGTGAGGGGAAAGGCCTTAAAGAGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCCCATAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGACCTTTCCAAAGCTg                                                                                   <  2:243806/149‑1 (MQ=255)

                                                                          gTCCTTAAAGAGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCCCATAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGACCTTTCCAAAGCTGGAAATGTATCTGCATGa                                                                  >  1:340701/1‑149 (MQ=255)

                                                                            ccTTAAAGAGATGGCGAGCGAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCCCATAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGACCTTTCCAAAGCTGGAAATGTATCTGCATGAAg                                                                >  2:420968/1‑149 (MQ=255)

                                                                              ttAAAGAGATGGCAAGGCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCCCATAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGACCTTTCCAAAGCTGGAAATGTATCTGCCTGAAGca                                                              >  1:436573/1‑149 (MQ=255)

                                                                               gaaaGAGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCCCATAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGACCTTTCCAAAGCTGGAAATGTATCTGCATGAAGcac                                                             <  1:184613/148‑1 (MQ=255)

                                                                                 aaGAGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCCCATAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGACCTTTCCAAAGCTGGAAATGTATCTGCATGAAGcacgg                                                           >  1:230725/1‑147 (MQ=255)

                                                                                   gagaTTGCAATCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCCCATAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGACCTTTCCAAAGCTGGAAATGTATCTGCATGAAGCACAGAc                                                         <  2:418634/149‑1 (MQ=255)

                                                                                   gagaTGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCCCATAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGACCTTTCCAAAGCTGGAAATGTATCTGCATGACGCACAGAc                                                         >  2:439114/1‑149 (MQ=255)

                                                                                      aTGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCCCATAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGACCTTTCCAAAGCTGGAAATGTATCTGCATGAAGCACAGACcca                                                      <  2:340701/149‑1 (MQ=255)

                                                                                             gCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCCCATAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGACCTTTCCAAAGCTGGAAATGTATCTGCATGAAGCACAGACCCACCAGTTa                                               >  1:347407/1‑149 (MQ=255)

                                                                                                agcagGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCCCATAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGACCTTTCCAAAGCTGGAAATGTATCTGCATGAAGCACAGCCCCACCAGTTACTg                                            >  2:1200/1‑149 (MQ=255)

                                                                                                agcagGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCCCATAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGACCTTTCCAAAGCTGGAAATGTATCTGCATGAAGCACAGACCCACCAGTTACTg                                            <  1:395453/149‑1 (MQ=255)

                                                                                                  cagGGGGAGCCGATGTCGGGAGCGCTGCAATTTGGTTTGATTCCCATAGTTGGATCGTACCTGCTACCGCATATTAGCCCTATGCTGCACCAGACCTTTCCAAAGCTGGAAATGTATCTGCATGAAGCACATACCCACCAGTTGCTGgc                                          <  2:9569/149‑1 (MQ=255)

                                                                                                  cagGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCCCATAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGACCTTTCCAAAGCTGGAAATGTATCTGCATGAAGCACAGACCCACCAGTTACTGgc                                          <  2:347407/149‑1 (MQ=255)

                                                                                                             gATGTCCGGACCGCTGCACATTGGTTTGATTCCCATAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGACCTTTCCAAAGCTGGAAATGTATCTGCATGAAGCACAGACCCACCAGTTACTGGCGCAACTGGACa                               <  1:400241/149‑1 (MQ=255)

                                                                                                                gTCCGGAACGCTGCACGGTGGGTTGGTTCCCGTAGTTGGACCGTAACTGGTACCGCATATTATCCCTATGCTGCACCAGTCCTTTCCGAAGCTGGAAATGTATCTGCATGAAGCACAGGCCCACCAGTTACTGGCGCAACTGGACAGCg                            <  2:356481/149‑1 (MQ=255)

                                                                                                                 tCCGGACCGCTGCACATTGGTTTGATTCCCATAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGACCTTTCCAAAGCTGGAAATGTATCTGCATGAAGCACAGACCCACCAGTTACTGGCGCAACTGGACAGCgc                           >  2:369219/1‑148 (MQ=255)

                                                                                                                                aTTGGTTTGATTCCCATAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGACCTTTCCAAAGCTGGAAATGTATCTGCATGAAGCACAGACCCACCAGTTACTGGCGCAACTGGACAGCGGCAAACTCGATTGCGt            >  1:137994/1‑149 (MQ=255)

                                                                                                                                          ttCCCATAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCGCCAGACCTTTCCAAAGCTGGAAATGTATCTGCATGAAGCACGGACCCACCAGTTACTGGCGCAACTGGGCAGCGGCAAACTCGATTGCGTGGTCCTcgcg  >  2:10797/1‑149 (MQ=255)

GCCGTAAAGTGTTGTTCACCCAGGCGGGAATGCTGCTGGTGGATCAGGCGCGTACCGTGCTGCGTGAGGTGAAAGTCCTTAAAGAGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCCCACAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGACCTTTCCAAAGCTGGAAATGTATCTGCATGAAGCACAGACCCACCAGTTACTGGCGCAACTGGACAGCGGCAAACTCGATTGCGTGATCCTCGCG  >  NC_000913_3_pae_tpiA/4158560‑4158846

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 8 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A