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
A9 F31 I1 R1	23	27.0	1176898	90.0%	1059208	142.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,196,220	C→T	H366H (CAC→CAT)	icd →	isocitrate dehydrogenase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,196,220	0	C	T	94.4%	36.6 / ‑5.4	18	H366H (CAC→CAT)	icd	isocitrate dehydrogenase
Reads supporting (aligned to +/- strand): ref base C (0/0); major base T (8/9); minor base G (0/1); total (8/10)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.49e-01

TCGCCCCTGGTGCAAACATCGGTGACGAATGCGCCCTGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTAT  >  NC_000913/1196087‑1196295

tcgCCCCTGGTGCAAACATCGGTGACGAATGCGCCCTGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATAGGGGTggg                                                                    >  1:176305/1‑143 (MQ=255)

 cgCCCCTGGTGCAAACATCGGTGACGAATGCGCCCTGTTTGAAGCCACCCACGGTACTGCGGCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGa                                                                   <  2:179184/143‑1 (MQ=255)

        ggTGCAAACAGCGGTGACGAATGCGCCCTGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGc                                                            <  1:393120/143‑1 (MQ=255)

          tGCAAACATCGGTGACGAATGCGCCCTGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGCGGTGAGGCTGCGCCATATGGGTTGGACTGAAGCgg                                                          >  1:132046/1‑143 (MQ=255)

                cagcGGTGACGAAGGCGCCCTGGTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGAcc                                                    <  2:73548/140‑2 (MQ=39)

                cagcGGGGACGCATGCGCCCTGTTTGGAGCCGCCCACGGTACTGCGCCGAAATAGGCCGGCCAGGACAAAGTCTTTCCCGGCTCTATTATGCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGAcc                                                    <  2:283723/140‑2 (MQ=25)

                    ggTGACGAATGCGCCCTGTTTGAAGGCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGAGGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGAcctgat                                                <  2:46254/143‑6 (MQ=38)

                           aaggcgcCCTGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTGTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTaaa                                         <  1:542157/140‑1 (MQ=38)

                            gggcgcgcTGTTTGAGGCCACCCACGGTACTGCGCCGAAATATGCCGGGCAGGACAAAGTAAATCCTGGCTCTCTTAAGCTCTTCGCGGAGATGATGCTGCGGCAGATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAg                                        <  1:24948/141‑1 (MQ=25)

                                          aaGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCa                          >  1:529460/1‑143 (MQ=25)

                                          aaGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGATGACCTGATTGTTCAAGGTATGGAAggagaa                          >  2:184975/1‑139 (MQ=37)

                                                cccacGGTACTGCGCCGAAATATGCCGATCAGGAGAAGGTAGATACGGGCTCGATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTGGGACTGAGGCGGCTGACCTGATTGTTGAAGGTATGGGAGGGgcaagcaat                    >  1:498369/1‑142 (MQ=255)

                                                 ccacGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCaatg                   >  2:299150/1‑141 (MQ=255)

                                                  cacGGTAGTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAAtgc                  <  1:246306/143‑1 (MQ=21)

                                                          tGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGCTTGTTGAAGGTGTGGAAGGCGCAATCAGTGCCAAGACCg          >  2:532604/1‑143 (MQ=18)

                                                            cgcCGAAATCTGCCGGTCACGACAAAGTAAGTCCTGGCTCGCTTGTTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTTGACTGCAGCGGCTCACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTa        <  2:578208/143‑1 (MQ=17)

                                                               cGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAAACCGTAAct     >  2:155250/1‑142 (MQ=18)

                                                                  catatGCCTGGCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGACGACGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTTATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCGTAACTTAt  <  1:332473/142‑1 (MQ=14)

TCGCCCCTGGTGCAAACATCGGTGACGAATGCGCCCTGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACCTAT  >  NC_000913/1196087‑1196295

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 8 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A