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
A32 F46 I1 R1	7	22.1	778232	90.7%	705856	146.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913_3_vch_pgi	4,296,384	+GC	intergenic (+587/+55)	gltP → / ← yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913_3_vch_pgi	4,296,383	1	.	C	92.9%	30.3 / ‑2.7	14	intergenic (+586/+56)	gltP/yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
Reads supporting (aligned to +/- strand): ref base . (0/1); new base C (4/9); total (4/10)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
*	NC_000913_3_vch_pgi	4,296,383	2	.	G	92.9%	24.9 / ‑2.6	14	intergenic (+586/+56)	gltP/yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
Reads supporting (aligned to +/- strand): ref base . (0/1); new base G (4/9); total (4/10)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.39e-01

GCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTT‑‑A‑‑CCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAGGTTCAACCAGT  >  NC_000913_3_vch_pgi/4296302‑4296512

||

gCTTAACGCGTCTTATCAGGCCTACGCCAGAAAGCGCATTAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTT‑‑ACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTg                                                                  <  1:168605/149‑1 (MQ=11)

       gcgTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGGGATTTTGTAGGTCGGATAAGGCGTTT‑‑ACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAAtt                                                           >  2:295119/1‑149 (MQ=255)

        cgTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTT‑‑ACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAAttt                                                          <  2:73127/149‑1 (MQ=255)

            ttATCAGGCCTACGCCAGACAGCGAAATAGCCTGATTTGGCGTGCTTTTAATGGTCGGATAAGGCGTTT‑‑ACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCa                                                      <  1:127261/149‑1 (MQ=14)

                             gACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTT‑‑ACGCCGCATCCGACATCAATGCCTGAGGCGACGCTTGCCGCGTCGTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGt                                     >  1:358645/1‑149 (MQ=17)

                              aCAGAGCAATAGCCTGATTTAGCATGATTTTGTAGGTCGGATAAGGCGTTTCCG‑‑CCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTa                                    <  2:335804/149‑1 (MQ=18)

                                         gCCTGATTTAGCGTGATTGTGTAGGTCGGATAAGGCGTTT‑‑ACGCCGCATCCGACATCAATGCCTGATGCGACGCTTTCCGCGTCGTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTc                         <  1:247778/149‑1 (MQ=21)

                                            tGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTT‑‑ACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTccct                      >  1:196991/1‑147 (MQ=255)

                                               tttAGCGTGATTTTGTAGGTCGGATAAGGCGTTT‑‑ACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACa                   <  2:237447/149‑1 (MQ=255)

                                               ttgaGCGTGATTTTGGAGGTCGGATAAGGCGTTT‑‑ACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACa                   <  2:148866/146‑1 (MQ=21)

                                                ttAGCGTGATTTTGTAGGTCGGATAAGGCGTTT‑‑ACGCCGCATCCGAAATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAg                  <  2:214583/149‑1 (MQ=255)

                                                     gTGATTTTGTAGGTCGGATAAGGCGTTT‑‑ACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAg             <  1:257965/149‑1 (MQ=255)

                                                           ttGTAGGTCGGATAAGGCGTTT‑‑ACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAGGTTCaa       <  1:256964/149‑1 (MQ=255)

                                                                ggTCGGATAAGGCGTTT‑‑ACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTCTTCCAGCCCGTCACACCCGGTATCAAACCCTTCCATACAGCTCAGGTTAAACCAGt  >  1:303573/1‑149 (MQ=21)

||

GCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTT‑‑A‑‑CCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAGGTTCAACCAGT  >  NC_000913_3_vch_pgi/4296302‑4296512

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A