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
A13 F89 I2 R1	21	29.0	1055738	89.7%	946996	142.8

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,296,381	+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	4,296,380	1	.	C	93.3%	34.8 / ‑3.4	15	intergenic (+586/+56)	gltP/yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
Reads supporting (aligned to +/- strand): ref base . (1/0); new base C (5/9); total (6/9)
Fisher's exact test for biased strand distribution p-value = 4.00e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
*	NC_000913	4,296,380	2	.	G	93.3%	35.3 / ‑3.4	15	intergenic (+586/+56)	gltP/yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
Reads supporting (aligned to +/- strand): ref base . (1/0); new base G (5/9); total (6/9)
Fisher's exact test for biased strand distribution p-value = 4.00e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCG‑T‑TTA‑‑CCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAGGTTCAA  >  NC_000913/4296302‑4296504

||

tgaCGCGTCGTATCAGGCCCACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCG‑T‑TTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCg                                                                <  1:481155/141‑1 (MQ=11)

        cTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCG‑T‑TTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTaa                                                        <  1:369040/143‑1 (MQ=255)

        cTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCG‑T‑TTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTaa                                                        <  1:399806/143‑1 (MQ=255)

              aGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCG‑T‑TTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTc                                                  <  1:273068/143‑1 (MQ=255)

              aGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCG‑T‑TTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTc                                                  <  1:517294/143‑1 (MQ=255)

              aGGCCTACGCCAGACAGCGCAATAGCCTGAGGTAGCGTGATTTTGTAGGCCGGATAAGGCG‑T‑TTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTc                                                  <  1:45462/143‑1 (MQ=14)

                     cGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCG‑T‑TTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCCTATCAGGCCTATCTTAACCGTTGGTAAATTTTCCCAActct                                           >  2:296655/1‑143 (MQ=14)

                                      gCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCG‑T‑TTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCaaa                          <  1:278379/143‑1 (MQ=255)

                                              tAGCGTGATTTTGTAGGTCGGATAAAGCGATATAA‑‑CCGCAGCCTACATCAATGCCTGATGCGACGCTGGCGGCTGCCTAGCAGACCGAGCTTAGCTTGTGAGTAATGTTGCAAACTCTGCACACCCGGGATCAAAcgcgtcac                  >  2:132911/1‑136 (MQ=9)

                                               aGCGTGATTTTGTAGGTCGGATAAGGCG‑T‑TTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTCGGTTAATTTTTCAAACTATTCACACCCGGTATCAAACCCTACCAt                 >  2:472641/1‑143 (MQ=18)

                                                 cGTGATTTTGTAGGTCGGATAAGGCG‑T‑TTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATAc               <  1:474335/143‑1 (MQ=255)

                                                       tttGTAGGTCGGATAAGGCG‑T‑TTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAACCTCTTCCCACCCGGTATCAAACCCTTCCATACAGCTCa         >  1:421975/1‑143 (MQ=21)

                                                          gTAGGTCGGGTAAGGCG‑T‑TTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAGGt      <  2:202084/143‑1 (MQ=255)

                                                              gTCGGATAAGGCG‑T‑TTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTCTCAGGCCTATCTTAACCGCTGGTTAATTTTTCAAACTCTTCACACCCGGGATCAAACCCTTCCACACAGCTCAggcccaa  >  2:190061/1‑138 (MQ=21)

                                                              attggATAATGCG‑T‑TTACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCACGTCTATCTTAACCGTTGGTTAATTTTTCAAACCCTTCACACCCGGTATCAAACCCATCCATACCGCTCACGTTCaa  >  2:78494/4‑143 (MQ=21)

||

TAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCG‑T‑TTA‑‑CCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAGGTTCAA  >  NC_000913/4296302‑4296504

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 8 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A