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 F5 I0 R1	24	41.2	1474486	89.7%	1322613	148.8

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913_3_pae_tpiA	3,528,907	A→T	24.1%	D80V (GAT→GTT)	yrfG →	GMP/IMP nucleotidase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913_3_pae_tpiA	3,528,907	0	A	T	24.1%	51.9 / 8.7	32	D80V (GAT→GTT)	yrfG	GMP/IMP nucleotidase
Reads supporting (aligned to +/- strand): ref base A (14/10); new base T (2/6); total (16/16)
Fisher's exact test for biased strand distribution p-value = 2.20e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGGCAAAAGCTGGTGCCTGAAACATGGGGCGCGAAAAACGGGGTTACGCCACAGGAAGCGATGGAATATATGCGCCAGCAATATCACGACGTACAGCATACGCTAAACTGGTACTGTCTTGATTACTGGAGTGAGCAACTGGGTCTGGATATCTGTGCGATGACCACCGAGATGGGACCGCGTGCCGTACTGCGTGAAGATACCATTCCGTTTCTTGAGGCACTGAAAGCCAGCGGTAAGCAGCGAATTTTGCTCACCAATGCGCATCCGCACAACCTGGCGGTAAAACTTGAG  >  NC_000913_3_pae_tpiA/3528759‑3529052

tGGCAAAAGCTGGTGCCGGAAACATGGGGCGCGAAAAACGGGGTTACGCCACAGGAAGCGATGGAATATATGCGCCAGCAATATCACGACGTACAGCATACGGTAAACTGGTACTGTCTTGATTACTGGAGTGAGCAACTGGGTCTGGa                                                                                                                                                   <  2:441230/149‑1 (MQ=255)

     aaaGCTGGTGCCTGAAACATGGGGCGCGAAAAACGGGGTTACGCCACAGGAAGCGATGGCATATATGCGCCAGCAATATCACGGCGTAAATCATTCGCTAAACTGGTACTGTCTTGATTACTGGAGTGAGCAACTGGGTCTGGatattt                                                                                                                                              >  1:350722/1‑147 (MQ=255)

     aaaGCTGGTGCCTGAAACATGGGGCGCGAAAAACGGGGTTACGCCACAGGAAGCGATGGAATATATGCGCCAGCAATATCACGACGTACAGCATACGCTAAACTGGTACTGTCTTGATTACTGGAGTGAGCAACTGGGTCGGGTTGTCt                                                                                                                                              >  1:274471/1‑149 (MQ=255)

           ggTGCCTGAAAGATGGGGCGCGAAAACCGGGGTTACGCCACAGGAAGCGTTGGGATATATGCGCCAGCAATATCACGACGTACAGCAGACGCTAAACTGGTACTGTCTTGATTACTGGAGTGAGCAACTGGGTCTGGATATCTGTGCGa                                                                                                                                        <  1:464986/149‑1 (MQ=255)

            gTGCCTGAAACATGGGGCGCGAAAAACGGGGTTGCGCCACAGGAAGCGATGGAATATATGCGCCGGCAATGTTACGACGTACAGCATACGCTAAACTGGTACTGTCTTTATTACTGGAGTGAGCAACGGGGTCTGGTTATCtttacgtt                                                                                                                                       >  2:160384/1‑142 (MQ=255)

             tGCCTGAAACATGGGGCGCGAAAAACGGGGTTACGCCACAGGAAGCGATGGAATATATGCGCCAGCAATATCACGACGTACAGCATACGCTAAACTGGTACTGTCTTGATTACTGGAGTGAGCAACTGGGTCTGGATATCTGTGCGATg                                                                                                                                      >  1:645096/1‑149 (MQ=255)

                cTGAAACATGGGGCGCGAAAAACGGGGTTACGCCACAGGAAGCGATGGAATATATGCGCCAGCAATATCACGACGTACAGCATACGCTAAACTGGTACTGTCTTGATTACTGGAGTGAGCAACTGGGTCTGGATATCTGTGCGATGacc                                                                                                                                   >  2:177824/1‑149 (MQ=255)

                 tGAAACATGGGGCGCGAAAAACGGGGTTACGCCACAGGAAGCGATGGAATATATGCGCCAGCAATATCACGACGTACAGCATACGCTAAACTGGTACTGTCTTGATTACTGGAGTGAGCAACTGGGTCTGGATATCTGTGCGATGacca                                                                                                                                  >  1:448556/1‑149 (MQ=255)

                      cATGGGGCGCGAAAAACGGGGTTACGCCACAGGAAGCGATGGAATATATGCGCCAGCAATATCACGACGTACAGCATACGCTAAACTGGTACTGTCTTGATTACTGGAGGGAGCAACTGGGTCTGGAGATCTGTGCGATGACCACCcag                                                                                                                             >  1:391964/1‑149 (MQ=255)

                       aTGGGGCGCGAAAAACGGGGTTACGCCACAGGAAGCGATGGAATATATGCGCCAGCAATATCACGACGTACAGCATACGCTAAACTGGTACTGTCTTGATTACTGGAGTGAGCAACTGGGTCTGGATATCTGTGCGATGACCACCgaga                                                                                                                            >  1:122451/1‑149 (MQ=255)

                                        gggTTCCTCCACCGGAAGCGATGGAATATATGCGCCAGCATTCTGACGACGTACAGCATACGCTACACTGGTACTGTCTTGATTACTGGAGTGAGCAACTGGGTTTTTTTAATGCTGCGGCGACCACCTATATGGTACCGCGTGCCGtc                                                                                                           <  2:581887/149‑2 (MQ=255)

                                        gggTTACGCCACAGGAAGCGATGGAATGTATGCGCCAGCAATATCACGACGTACAGCATACGCTAAACTGGTACTGTCTTGATTACTGGAGTGAGCAACTGGGTCTGGATATCTGTGCGATGACCACCGAGATGGGACCGCGTGCCGTa                                                                                                           <  1:378386/149‑1 (MQ=255)

                                         ggTTACGCCACAGGAAGCGATGGAATATATGCGCCAGCAATATCACTACGTACAGCATACGCTAAACTGGTACTGTCTTGATTACTGGAGTGAGCAACTTTTTTTTTTTAATGATGCGGCGACCACCGAGATGGGACCGCGTGCCGTAc                                                                                                          <  2:721698/149‑1 (MQ=255)

                                                 cacaGTAAGCGATGGTATATGTGCGCTCGCATTACCACGACGGATCGCATACGCTATATTGGTACTGTGTTGATTCCTGGAGTGAGCAACTTGGTTTTTTTATTGGTGCGGCGACCACCGAGATGGGACCGCGTGCCGTACTGCGTGaa                                                                                                  <  2:461466/149‑1 (MQ=255)

                                                      gAAGCGGTTGCATATGTGCGCCAGGAATATCGACATGTAGAGCATATGCTACACTTGTACTGTTTTGATGACGGGAGTGATCAATTTGTTTTTTTTAATGATACGGTGACCACCGAGATGGGACCGCGTGCCGTACTGCGTGAAGATAc                                                                                             <  2:412436/149‑1 (MQ=255)

                                                                  tatatGGTCCATCAATATAACGACGTACATCATACGTGAAACTGTGAATGACTTGATTACTGGAGTGGGCTACTTTTTTTTTTTAATGATACGGCGACCACCGAGATGGGACCGCGTGCCGTACTGCGTGAAGATACCATTCCGTTTCt                                                                                 <  2:162444/149‑1 (MQ=255)

                                                                     atGCGCCAGCAATATCACGACGTACAGCATACGCTAAACTGGTACTGTCTTGATTACTGGAGTGAGCAACTGGGTCTGGATATCTGTGCGATGACCACCGAGATGGGACCGCGTGCCGTACTGCGTGAAGATACCATTCCGTTTCTTGa                                                                              >  1:288050/1‑149 (MQ=255)

                                                                                     acgacgTACAGCATACGCTAAACTGGTACTGTCTTGATTACTGGAGTGAGCAACTGGGTCTGGATATCTGTGCGATGACCACCGAGATGGGACCGCGTGCCGTACTGCGTGAAGATACCATTCCGTTTGTTGAGGCACTGAAAGCCAGc                                                              >  1:82428/1‑149 (MQ=255)

                                                                                             ccgCATACGCTAATCTGGTACTGTCTTGATTACTGGAGTGATCAACTGGGTCTGGATATCTGTGCGATGACCACCGAGATGGGACCGCGTGCCGTACTGCGTGAAGATACCATTCCGTTTCTTGAGGCACTGAAAGCCAGCGGTAagca                                                      <  1:202683/147‑1 (MQ=255)

                                                                                               gCATACGCTAAACTGGTACTGTCTTGATTACTGGAGTGAGCAACTGGGTCTGGATATCTGTGCGATGACCACCGAGATGGGACCGCTTGCCGTACTAAGAAACGATAGGATTCCGTTTCTTGAGGCACTGAAAGCCAGCGGTAagcagc                                                    <  1:726644/149‑1 (MQ=255)

                                                                                                            tGGTACTGTCGTGTTTCCTGGTGTGAGCAAGTTGTTTTTTTTAATGATGCGGCGACCACCGAGATGGGACCGCGTGCCGTACTGCGTGAAGCTACCATTCCGTTTCTTGAGGCACTGAAAGCCAGCGGTAAGCAGCGAATTTTGCTCAc                                       <  2:708634/149‑1 (MQ=255)

                                                                                                               tACTGTCTTGATTACTGGAGTGAGCAACTGGGTCTGGATATCTGTGCGATGACCACCGAGATGGGACCGCGTGCCGTACTGCGTGAAGATACCATTCCGCTTCTTGAGGCACTGAAAGCCAGCGGTAGGCAGCGAGTTTTGCTccccca                                    >  1:16896/1‑147 (MQ=255)

                                                                                                                      ttGATTACTGGAGTGAGCAACTGGGTCTGGATATCTGTGCGATGACCACCGAGGTGGGACCGCGTGCCGTACTGCGTGAAGATACCATTCCGTACCTTGAGGCACTAAAAGACAGAGGTAAGCAGCGACTATTGCCCGCCAATgtacat                             >  2:126123/1‑144 (MQ=255)

                                                                                                                      ttGATTACTGGAGTGAGCAACTGGGTCTGGATATCTGTGCGATGACCACCGAGATGGGACCGCGTGCCGTACTGCGTGAAGATACCATTCCGTTTCTTGAGGCACTGAAAGCCAGCGGTAAGCAGCGAATTTTGCTCACCAATGCGCAt                             >  1:259781/1‑149 (MQ=255)

                                                                                                                      ttGATTACTGGAGTGAGCAACTGGGTCTGGATATCTGTGCGATGACCACCGAGATGGGACCGCATGCCGTACTGCGTGAAGATACCATTCCGTTTCTTGAGGCACTGAAAGCCAGCGGTAAGCAGCGAATTTTGCTCACCAATGCGCAt                             >  1:694384/1‑149 (MQ=255)

                                                                                                                         aTTACTGGAGTGAGCAGCGGGGTCGGGAGCTCTGCGCGATGCCCACCGAGAGGGGACCGCGTGCCGTACTGCGTGAAGATACCATTCCGTTTCTTGAGGCACTGAAAGCCAGCGGTAAGCAGCGAATTTTGCTCACCAATGCGCATCCg                          <  1:708597/149‑1 (MQ=255)

                                                                                                                          ttACTGGAGTGAGCAACTGGGTCTGGATATCTGTGCGATGACCACCGAGATGGGACCGCGTGCCGTACTGCGTGTAGATACCATTCCGTTTCTTGAGGCACTGAAAGCCAGCGGTAAGCAGCGAATTTTGCTCACCAATGCGCATCCGc                         <  1:674491/149‑1 (MQ=255)

                                                                                                                             cTGGAGTGAGCAACTGGGTCTGGATATCTGTGCGATGACCACCGAGATGGGACCGCGTGCCGTACTGCGTGAAGATACCATTCCGTTTCTTGAGGCACTGAAAGCCAGCGGTAAGCAGCGAATTTTGCTCACCAATGCGCATCCGcaca                      >  1:386746/1‑149 (MQ=255)

                                                                                                                                gAGTGAGCAACTGGGTCTGGATATCTGTGCGATGACCACCGAGATGGGACCGCGTGCCGTACTGCGTGAAGATACCATTCCGTTTCTTGAGGCACTGAAAGCCAGCGGTAAGCAGCGAATTTTGCTCACCAATGCGCATCCACACAAcc                   >  1:646041/1‑149 (MQ=255)

                                                                                                                                 aGTGAGCAACTTGTTCTGTATAACTGTGCGGTGACCACCGAGATGGGACCGCGTGCCGTACTGCGTGAAGATACCATTCCGTTTCTTGAGGCACTGAAAGCCAGCGGTAAGCAGCGAATTTTGCTCACCAATGCGCATCCGCACAACCt                  <  2:732867/149‑1 (MQ=255)

                                                                                                                                  gTGCGCAACTGGGTCTGGATATCTGTGCGATGACCACCGAGATGGGACCGCGTGCCGTACTGCGTGAAGATACCATTCCGTTTCTTGAGGCACTGAAAGCCAGCGGTAAGCAGCGAATTTTGCTCACCAATGCGCATCCGCACAACCTg                 <  1:419810/149‑1 (MQ=255)

                                                                                                                                    gAGCAACTGGGTCTGGATATCTGTGCGATGACCACCGAGATGGGACCGCGTGCCGTACTGCGTGAAGATACCATTCCGTTTCTTGAGGCACTGAAAGCCAGCGGTAAGCAGCGAATTTTGCTCACCAATGCGCATCCGCACAACCTGGc               <  1:177824/149‑1 (MQ=255)

                                                                                                                                       cAACTGGGTCTGGATATCTGTGCGATGACCACCGAGATGGGACCGCGTGCCGTACTGCGTGAAGATACCATTCCGTTTCTTGAGGCACTGAAAGCCAGCGGTAAGCAGCGAATTTTGCTCACCAATGCGCATCCGCACAACCTGGCGGt            >  1:419069/1‑149 (MQ=255)

                                                                                                                                                 tGGATATCTGTGCGATGACCACCGAGATGGGACCGCGTGCCGTACTGCGTGAAGATACCATTCCGTTTCTTGAGGCACTGAAAGCCAGCGGTAAGCAGCGAATTTTGCTCACCAATGCGCATCCGCACAACCTGGCGGTAAAACTTGAg  <  1:23627/149‑1 (MQ=255)

TGGCAAAAGCTGGTGCCTGAAACATGGGGCGCGAAAAACGGGGTTACGCCACAGGAAGCGATGGAATATATGCGCCAGCAATATCACGACGTACAGCATACGCTAAACTGGTACTGTCTTGATTACTGGAGTGAGCAACTGGGTCTGGATATCTGTGCGATGACCACCGAGATGGGACCGCGTGCCGTACTGCGTGAAGATACCATTCCGTTTCTTGAGGCACTGAAAGCCAGCGGTAAGCAGCGAATTTTGCTCACCAATGCGCATCCGCACAACCTGGCGGTAAAACTTGAG  >  NC_000913_3_pae_tpiA/3528759‑3529052

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 8 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A