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
A15 F3 I0 R1	49	96.5	1638068	98.5%	1613496	272.5

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	4,296,189	A→G	31.4%	intergenic (+396/+248)	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	4,296,189	0	A	G	31.4%	9.0 / 5.8	19	intergenic (+396/+248)	gltP/yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
Reads supporting (aligned to +/- strand): ref base A (6/7); new base G (3/3); total (9/10)
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

ATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAA  >  NC_000913/4295902‑4296460

tttttgtacgcggtataagtgtgttACGCCGAGTCGGACGTCAACGCCTGATGCGACGCTGACCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTTTAGGTAGGATAAGGCGTTTACGCCGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTaa                                                                                                                                                                                                                                                                                <  1:615358/266‑1 (MQ=11)

     gTAGATCGGAGAAGGCGTTTATGCCGCATCCGACATAAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGt                                                                                                                                                                                                                                                                           <  1:558182/289‑1 (MQ=37)

               tAAGGCGTTTATGCCGCATCCGACATCAACGCCGGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTGGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGc                                                                                                                                                                                                                                                                 <  2:733693/289‑1 (MQ=37)

                aagggcgtgatgccggaggcggtaacAACGCCGGACAGGACGCTTACCGCGTCTTATCGGGGTTACGCCAGGATGCGCAATAGGCTGAGTCCGGCGGATTTAGTGGTACGGAGTGGGCGTGTAGGCCGCATCCGACGTCAACGCCTGTTGCGAGGCTTGGCGCGTCTTATCAGGGGTAGGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTGGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGc                                                                                                                                                                                                                                                                 <  1:145013/263‑1 (MQ=2)

                        tATGCCGCATCCGACATCAACGCCTGATGCGACGCTCAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAg                                                                                                                                                                                                                                                        >  2:699156/1‑289 (MQ=37)

                           tacgaggccggaaacAACGATTGATGAGGCGCTTGACTCGTCTTATCGGTCCGAAGTCATAGAGCGAAATAGCAGTATTTAGTGTGATTTTTTATGTCGGGTAGGGCGTTTCCGCCGCATCAGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACa                                                                                                                                                                                                                                                     <  1:189308/275‑1 (MQ=11)

                           gCCGCACCCGGCATCAACGCCTGATGCGACGCTTACCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACa                                                                                                                                                                                                                                                     <  1:638309/289‑1 (MQ=18)

                               cATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACCCTTAACGCGTCTTAAAAGCCCTACGCCACACAgcg                                                                                                                                                                                                                                                  >  1:309264/1‑288 (MQ=255)

                                 tCCGAAATAAATGCAGGATGGGACGATTAAGGCGGCTTATCAGGCTTACGCCAGACAGCGCAATAGCATGAGTTAGCGTGATTTTGTAGGGCGGATAAGGCGTTTACGCCGCATCCGACATCAACGCCGGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCaa                                                                                                                                                                                                                                               <  1:641326/289‑1 (MQ=11)

                                                   tGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGa                                                                                                                                                                                                                             >  1:260674/1‑289 (MQ=35)

                                                                                           cgcAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGCCAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCTCACATCAACCCCTGATGCGACGCTTACCGCGTCTTATCACGCCTCCGCTAGACACCGCCTTAGCCTTGTTTAGTGTGACTTTTTAGGTAGGATAAGTCATTTAAGCCGCACGCGACa                                                                                                                                                                                      >  1:93941/1‑288 (MQ=11)

                                                                                                                 aTTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACCTCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGCCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACCGCGCTATAGCCTGATTTAGCGTGCTTTTGTAGTTCGGATAAGGCGTTTAAGACGCTCCCGCCATCAATGCCTGATGCTACGCttt                                                                                                                                                                >  2:64465/1‑287 (MQ=11)

                                                                                                                                                                                                  cGCCAGACGGCGCGATATCCTGTTTTAGCGGGATTTTGTAGGTCGGTTAGGGCGTTTATGCCCAATCGGACATCAACGCCTGATGGTACGTTTAGCGGGCCTTATCAGGCTTAAGCCAGACAGCTCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTAACAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTAcgccg                                                                              <  1:518194/289‑1 (MQ=11)

                                                                                                                                                                                                                                                 tAAGGCGTTTCCGCCGCAGCCGACATCAACGCCTGTTGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCaatgcctgatgcgacgcttgccgcgtctaatcaggc                               >  2:15229‑M2/1‑253 (MQ=255)

                                                                                                                                                                                                                                                 tAAGGCGTTTACGCCGCATCCGACATCAACGCCTGATGCAACGCTCGCCGCGTCTTAGCAGGACTCCGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCCTCCGACATCAACGCCTGATGCGCCGCTTAACGCGTCTTATCAGGCCTACGCCCGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCaaggcctgatgcgacgcttgccgcgtcttatcaggc                               >  2:558942‑M2/1‑253 (MQ=255)

                                                                                                                                                                                                                                                  aaGGGGTTTACGCCGCATCTGACATCAACGCTGGATGCGACGCTTGCCGCGTCTTATCAGGCCCACGCCAGAGAGCGAAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCaatgcctgatgcgacgcttgccgcgtcttatcaggcc                              >  1:684903‑M2/1‑252 (MQ=255)

                                                                                                                                                                                                                                                                    ccGACATCAGCGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTa            <  2:274155/289‑1 (MQ=255)

                                                                                                                                                                                                                                                                      tgtttgaatgCCGGATGCGACGCTTGCCGCGTCTTATCATACTTACGCCAGCCAGCGCAATAGCCTGATTTGGCGTGATTTTGTAGGTCGGTTAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCTACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAATGCCTGATGAGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAAt          <  2:695402/280‑1 (MQ=11)

                                                                                                                                                                                                                                                                              cGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCaaa  <  2:173501/289‑1 (MQ=255)

                                                                                                                                                                                                                                                                               gCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCaa   >  1:798636/1‑287 (MQ=255)

ATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAA  >  NC_000913/4295902‑4296460

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 8 ≤` `ATCG/ATCG` `< 10 ≤` `ATCG/ATCG` `< 25 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A