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
A29 F119 I1 R1	30	31.1	1326154	90.1%	1194864	128.4

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	95.0%	34.1 / ‑6.9	20	H366H (CAC→CAT)	icd	isocitrate dehydrogenase
Reads supporting (aligned to +/- strand): ref base C (0/0); major base T (12/7); minor base G (1/0); total (13/7)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.77e-01

TCGGTGACGAATGCGCCCTGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACC  >  NC_000913/1196105‑1196292

tCGGTGACGAATGCGCCCTGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGCCAAAGTAAATCCTGGCTCTATCATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGActg                                                             >  2:446130/1‑127 (MQ=255)

 cGGTGACGAATGCGCTCTGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGActga                                                            <  2:31992/129‑4 (MQ=255)

 cGGTGACGAATGCGCCCTGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGa                                                            >  2:148053/1‑129 (MQ=255)

       cGAATGCGCCCTGTTTGAAGCCACCCACGATACTGCGCCGAAATATGCCGGTCAGGAAAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCACCATATGGGTTGGACTGaaacagc                                                      >  2:148910/1‑124 (MQ=255)

        gAATGCGCCCTGTTTGCAGCCACCCACGGTACTACGCCGAAATATACCGATCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCt                                                     >  1:223218/1‑129 (MQ=38)

        gAATGCGCCCTGTTTGAAGCCAGCCACGGTACTGTGCCGGAATATGTCGGTCAGGACAAAGTAAATCCTGGCTCTTTTATTCTTTCCGCTGAGTTCATGCTGCGCAATATGGGTTGGACTGAAGCGGCt                                                     <  1:624947/129‑1 (MQ=255)

          aTGCGCCCTGTTTGCAGCCCCCCACGGTACTGCGCCGAAATAAACAAAACAAAAAAAAGTAAATCCTGGCTCTATTATTCTCACCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGa                                                   >  1:100846/1‑129 (MQ=25)

                       gAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTaaa                                      <  2:226017/129‑1 (MQ=37)

                            cacccacGGTACTGCGCCGCACTATGCCGGTCAGGACAAAATAAATCATAGCTCTATTATTCTCTCAGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTAt                                 >  1:427222/1‑129 (MQ=21)

                            cacccacGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTCTTAAAGGTAt                                 >  2:594435/1‑129 (MQ=37)

                                cacGGTACTGCGCCGCAATATGCCGGTCAGGACAAAAAAAATAAAAGCACTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGaa                             >  1:474769/1‑129 (MQ=18)

                                  cGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGATATGATTCTGTTCCATATGTGTTTGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAgg                           <  1:251735/129‑1 (MQ=25)

                                      aCTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGTGGCTGACCGGATTGTCAAAGCAGTGGAAGccgga                       >  2:568394/1‑127 (MQ=25)

                                                 atatGCCTGTCAGGACAAAGTAAATCCTTGCTCTATTATTCTCTCCGCTGAGATGATGCTGTGCTATTTGTGTTTGTCTTAATCGGCTGATCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCaa            <  1:184547/129‑1 (MQ=16)

                                                      ccGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCg       >  2:107393/1‑129 (MQ=17)

                                                      ccGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAATGCCAAGACCg       >  2:460575/1‑129 (MQ=17)

                                                         gTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGTTGTCTTTTTTTTTATTTTTTTGGAAGGCGCAATCAAGGCCAAGACCGTaa    <  1:279013/129‑1 (MQ=18)

                                                         gTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATACTGCGCCATATGGGTTGGACTGAAGCGGCTGACCTGATTGTTAAAGGCATCGAAGGCGCAGTCAATGCCAAGAcccgaa    >  2:26482/1‑125 (MQ=17)

                                                          tCAGGACAAAGTAAATCCTGGCTCTATTATTCTCCCCGCTGAGATGATGCTGCGCCATATGGGTTGGACTGAAGCGGCTGTCCTTTTTTTTTTTGGTATGGAAGGCGCAAGCAATGCCAAGACCGGAAc   <  1:299885/129‑1 (MQ=12)

                                                           cAGGAAAAAGTAAATCCTGGCTCTAAAATTCACGCCGCGGAGATGATGCTGCACCAGATGGGTTGGACTGAAGCGCCTGACCTGATTGTTAAAGGTAAGGAAGGGGCAATCACAGCAAAACACGTAAcg  >  2:261040/1‑128 (MQ=9)

TCGGTGACGAATGCGCCCTGTTTGAAGCCACCCACGGTACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAATCCTGGCTCTATTATTCTCTCCGCTGAGATGATGCTGCGCCACATGGGTTGGACCGAAGCGGCTGACTTAATTGTTAAAGGTATGGAAGGCGCAATCAACGCGAAAACCGTAACC  >  NC_000913/1196105‑1196292

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A