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
A11 F44 I0 R1	115	55.9	2109214	91.7%	1934149	142.3

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	1,196,232	C→T	47.7%	T370T (ACC→ACT)	icd →	isocitrate dehydrogenase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,196,232	0	C	T	47.7%	7.5 / 25.4	29	T370T (ACC→ACT)	icd	isocitrate dehydrogenase
Reads supporting (aligned to +/- strand): ref base C (7/8); new base T (6/8); total (13/16)
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

CCTGGTGCAAACATCGGTGACGAATGCGCCCTGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAA  >  NC_000913/1196092‑1196373

ccTGGTGCAAACATCGGTGACGAATGCGCCCTGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGa                                                                                                                                             >  1:514156/1‑143 (MQ=255)

 cTGGTGCAAACATCGGTGACGAATGCGCCCTGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGaa                                                                                                                                            <  1:312963/143‑1 (MQ=255)

   ggTGCAAACATCGGTGACGAATGCGCCCTGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTAAGGACAAAGTAAATACTGGCTCTATTATTTTCTCCGCTGAGATGATGCTGCGCGATATGGGTTGGGCTGAAGc                                                                                                                                          >  2:686955/1‑143 (MQ=255)

     tGCAAACATCGGTGACGAATGCGCCCTGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCgg                                                                                                                                        <  1:301837/143‑1 (MQ=255)

               ggTGACGAATGCGCCCTGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGATGAcctgat                                                                                                                              >  1:272294/1‑138 (MQ=255)

                 tGACGAATGCGCCCTGTTTGCCGCCACCCACGAAACCGTGCTTAACAGGGCCTGGCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGACGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTg                                                                                                                            <  1:1038908/143‑1 (MQ=255)

                   aCGAATGCGCCCTGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGtt                                                                                                                          <  2:426705/143‑1 (MQ=38)

                                gTTTGAAGCCACCCGCGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTATATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGTTGACCTGATTGTTAAAGGTATGGAAg                                                                                                             <  2:1003384/143‑1 (MQ=25)

                                  ttGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCCCTCCGCTGAGAGGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGgc                                                                                                           <  1:748891/143‑1 (MQ=25)

                                     aaGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAGTTGTTAAAGGTATGGAGGGCGCa                                                                                                        >  1:423285/1‑143 (MQ=255)

                                          acccacGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGACATGATGCTGCGGCACATGGGTTGGACCGAAGCGGCGGGATTAATTATTGAAGGTCGTGAAGGCGCAATCac                                                                                                   >  2:738424/1‑142 (MQ=255)

                                          aaccacGGTACTGCGCGTGCATATGTCGTTCAGGACAGAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATTGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCaa                                                                                                   <  2:960797/141‑1 (MQ=18)

                                            ccacGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATCTGGGTTGGACTGAAGCGGCTTACCTGATCTTTATCGTTATGTAAGGCGTATTCaatg                                                                                                 >  1:290778/1‑141 (MQ=25)

                                            ccacGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTGATTGTTAAAGGTATGGAAGGCGCAATCAAcg                                                                                                 >  1:793774/1‑143 (MQ=255)

                                             cacGGTACTGCGCCGAAATACGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCTATACGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAAtgc                                                                                                <  1:604930/143‑1 (MQ=21)

                                                ggTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAGATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCaa                                                                                             <  2:932884/143‑1 (MQ=21)

                                                ggTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAAtgccaa                                                                                             >  1:730939/1‑140 (MQ=21)

                                                ggTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCAGAGATGATGCTGCGCCACATGGGTTGGACCGAAGAGACTGACATAATTGTTAAAGGTATGGAAGGCGCAATCAACACGaa                                                                                             >  2:446857/1‑143 (MQ=38)

                                                  tACTGCGCCGAAATATGCCCGGCAGGACAAAGTACATCCTGGCCCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGaaaa                                                                                           <  1:390242/143‑1 (MQ=255)

                                                    cTGCGCGTAAATATGCCGGTCAGGACAAAGTAAATCCCGCCTCTATTCTTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAAcc                                                                                         <  2:733438/143‑1 (MQ=37)

                                                         ccGAAATATGCCGGTCAGGACAAAGTAAATCGTGGCTCGATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAAc                                                                                    <  2:654531/143‑1 (MQ=255)

                                                         ccGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAAc                                                                                    >  2:947620/1‑143 (MQ=255)

                                                           gAAATATGCCGGTCAGTACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCt                                                                                  <  1:816800/143‑1 (MQ=255)

                                                                   ccGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTATGACTTc                                                                          >  1:4471/1‑143 (MQ=17)

                                                                                        cTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCt                                                     >  1:989879/1‑143 (MQ=255)

                                                                                           gCTCGATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTaaa                                                  <  2:825754/143‑1 (MQ=255)

                                                                                                                            gcCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGatc                 >  1:663129/1‑143 (MQ=255)

                                                                                                                                  tGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGaa           <  1:569386/143‑1 (MQ=255)

                                                                                                                                  tGGGTTGGACCGAAGCGGCTGACTTAACTGTTACAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGaa           <  2:532437/143‑1 (MQ=255)

                                                                                                                                           ccGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTag  >  2:793280/1‑142 (MQ=255)

                                                                                                                                           ccGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTaa  >  2:756407/1‑143 (MQ=255)

CCTGGTGCAAACATCGGTGACGAATGCGCCCTGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTATGACTTCGAGCGTCTGATGGATGGCGCTAAACTGCTGAAATGTTCAGAGTTTGGTGACGCGATCATCGAAAACATGTAA  >  NC_000913/1196092‑1196373

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A