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 F1 I1 R1	778	68.7	3228504	93.4%	3015422	109.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,211,652	C→T	intergenic (+75/+28)	icdC → / ← iraM	pseudogene, isocitrate dehydrogenase C‑terminal gene fragment, idcC' is a 54 codon 3' gene fragment created during e14 prophage insertion/RpoS stabilzer during Mg starvation, anti‑RssB factor

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,211,652	0	C	T	100.0%	98.0 / NA	31	intergenic (+75/+28)	icdC/iraM	pseudogene, isocitrate dehydrogenase C‑terminal gene fragment, idcC' is a 54 codon 3' gene fragment created during e14 prophage insertion/RpoS stabilzer during Mg starvation, anti‑RssB factor
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (14/17); total (14/17)

GAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGAAAACATGTAATCTCTCCATGTGTTAAATATTGAAACGGGCGTATAACACGCCCGTTGTTTTATTTATGTGGATATTATTAATAGCATATCGAGCATATTTATATGAAGCCCATTACTTGAGCCCATATGGGCATATTTTTATAATGCAACTATTATGTAAACATTTATTTGTTATTTTGCTTTCTCCTGGAGGACACTCTTGACTGCTTTTGAGTAAACT  >  NC_000913/1211518‑1211787

gAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGAAAACATGTAATCTCTCCATGTGTTAAATATTGAAACGGGCGTATAACACGCCCGTTGTTTTATTTATGTGGATATTATTAATAGTatat                                                                                                                                     <  1:1390174/139‑1 (MQ=255)

    gcgcTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGAAAACATGTAATCTCTCCATGTGTTAAATATTGAAACGGGCGTATAACACGCCCGTTGTTTTATTTATGTGGATATTATTAATAGTATATCGAg                                                                                                                                 <  2:1123184/139‑1 (MQ=255)

    gcgcTAAGCTGCTGAAATGTTCAGAGTTTAGTGAAGCGATCATCGAAAACATGTAATCTCTCCATGTGTTAAATATTGAAACGGGCGTATAACACGCCCGTTGTTTTATTTATGTGGATATTATTAATAGTATATCGAg                                                                                                                                 <  2:284021/139‑1 (MQ=255)

      gcTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGAAAACATGTAATCTCTCCATGTGTTAAATATTGAAACGGGCGTATAACACGCCCGTTGTTTTATTTATGTGGATATTATTAATAGTATATCGAGCa                                                                                                                               <  1:1428543/139‑1 (MQ=255)

                  aaaTGTTCAGAGTTTGGTGAAGCGATCATCGAAAACATGTAATCTCTCCATGTGTTAAATATTGAAACGGGCGTATAACACGCCCGTTGTTTTATTTATGTGGATATTATTAATAGTATATCGAGCATATTTATATGaa                                                                                                                   <  1:635939/139‑1 (MQ=255)

                                 ggTGAAGCGATCATCGAAAACATGTAATCTCTCCATGTGTTAAATATTGAAACGGGCGTATAACACGCCCGTTGTTTTATTTATGTGGATATTATTAATAGTATATCGAGCATATTTATATGAAGCCCATTACTTGAGc                                                                                                    >  2:697100/1‑139 (MQ=255)

                                                  agaCATGTAATCTCTCCATGTGTTAAATATTGAAACGGGCGTATAACACGCCCGTTGTTTTATTTATGTGGATATTATTAATAGTATATCGAg                                                                                                                                 >  1:966552/3‑93 (MQ=255)

                                                  aaaCATGTAATCTCTCCATGTGTTAAATATTGAAACGGGCGTATAACACGCCCGTTGTTTTATTTATGTGGATATTATTAATAGTATATCGAg                                                                                                                                 <  2:966552/93‑1 (MQ=255)

                                                       tGTAATCTCTCCATGTGTTAAATATTGAAACGGGCGTATAACACGCCCGTTGTTTTATTTATGTGGATATTATTAATAGTATATCGAGCATATTTATATGAAGCCCATTACTTGAGCCCATATGGGCATATTTTTATaa                                                                              <  1:918591/139‑1 (MQ=255)

                                                                    tgtgTTAACTATTGAAACGGGCGTATAACACGCCCGTTGTTTTATTTATGTGGATATTATTAATAGTATATCGAGCATATATATATGAAg                                                                                                                  >  2:1411448/1‑90 (MQ=255)

                                                                    tgtgTTAAATATTGAAACGGGCGTATAACACGCCCGTTGTTTTATTTATGTGGATATTATTAATAGTATATCGAGCATATTTATATGAAg                                                                                                                  <  1:1411448/90‑1 (MQ=255)

                                                                                tGAAACGGGCGTATAACACGCCCGTTGTTTTATTTATGTGGATATTATTAATAGTATATCGAg                                                                                                                                 <  2:1542615/63‑1 (MQ=255)

                                                                                tGAAACGGGCGTATAACACGCCCGTTGTTTTATTTATGTGGATATTATTAATAGTATATCGAg                                                                                                                                 >  1:1542615/1‑63 (MQ=255)

                                                                                tGAAACGGGCGTATAACACGCCCGTTGTTTTATTTATGTGGATATTATTAATAGTATATCGAGCATATTTATATGAAGCCCa                                                                                                              <  2:1427035/82‑1 (MQ=255)

                                                                                tGAAACGGGCGTATAACACGCCCGTTGTTTTATTTATGTGGATATTATTAATAGTATATCGAGCATATTTATATGAAGCCCa                                                                                                              >  1:1427035/1‑82 (MQ=255)

                                                                                tGAAACGGGCGTATAACACGCCCGTTGTTTTATTTATGTGGATATTATTAATAGTATATCGAGCATATTTATATGAAGCCCATTACtt                                                                                                        >  1:1341653/1‑88 (MQ=255)

                                                                                tGAAACGGGCGTATAACACGCCCGTTGTTTTATTTATGTGGATATTATTAATAGTATATCGAGCATATTTATATGAAGCCCATTACtt                                                                                                        <  2:1341653/88‑1 (MQ=255)

                                                                                                  cGCCCGTTGTTTTATTTATGTGGATATTATTAATAGTATATCGAGCATATTTATATGAAGCCCATTACTTGAGCCCATATGGGCATATTTTTATAATGc                                                                           <  1:1298938/99‑1 (MQ=255)

                                                                                                  cGCCCGTTGTTTTATTTATGTGGATATTATTAATAGTATATCGAGCATATTTATATGAAGCCCATTACTTGAGCCCATATGGGCATATTTTTATAATGc                                                                           >  2:1298938/1‑99 (MQ=255)

                                                                                                  cGCCCGTTGTTTTATTTATGTGGATATTATTAATAGTATATCGAGCATATTTATATGAAGCCCATTACTTGAGCCCATATGGGCATATTTTTATAATGCAACtatt                                                                    >  1:400942/1‑106 (MQ=255)

                                                                                                  cGCCCGTTGTTTTATTTATGTGGATATTATTAATAGTATATCGAGCATATTTATATGAAGCCCATTACTTGAGCCCATATGGGCATATTTTTATAATGCAACtatt                                                                    <  2:400942/106‑1 (MQ=255)

                                                                                                   gCCCGTTGTTTTATTTATGTGGATATTATTAATAGTATATCGAGCATATTTATATGAAGCCCATTACTTGAGCCCATATGGGCATATTTTTATAATGCAACTATTATGTAAACATTTATTTGTTATTTTGCTTTCTCCt                                  >  1:793449/1‑139 (MQ=255)

                                                                                                                   atGTGGATATTATTAATAGTATATCGAGCATATTTATATGAAGCCCATTACTTGAGCCCATATGGGCATATTTTTATAATGCAACTATTATGTAAACATTTATTTGTTATTTTGCTTTCTCCTGGAGGACACTCTTGAc                  <  2:793449/139‑1 (MQ=255)

                                                                                                                     gtgGATATTATTAATAGTATATCGAGCATATTTATATGAAGCCCATTACTTGAGCCCATATGGGCATATTTTTATAATGCAACta                                                                      <  2:1580679/85‑1 (MQ=255)

                                                                                                                     gtgGATATTATTAATAGTATATCGAGCATATTTATATGAAGCCCATTACTTGAGCCCATATGGGCATATTTTTATAATGCAACta                                                                      >  1:1580679/1‑85 (MQ=255)

                                                                                                                     gtgGATATTATTAATAGTATATCGAGCATATTTATATGAAGCCCATTACTTGAGCCCATATGGGCATATTTTTATAATGCAACTATTATGTAAACATTTATTTGTTATTTTGCTTTCTCCTg                                 <  2:318821/122‑1 (MQ=255)

                                                                                                                     gtgGATATTATTAATAGTATATCGAGCATATTTATATGAAGCCCATTACTTGAGCCCATATGGGCATATTTTTATAATGCAACTATTATGTAAACATTTATTTGTTATTTTGCTTTCTCCTg                                 >  1:318821/1‑122 (MQ=255)

                                                                                                                             tattaATAGTATATCGAGCATATTTATATGAAGCCCATTACTTGAGCCCATATGGGCa                                                                                         >  1:777431/1‑58 (MQ=255)

                                                                                                                             tattaATAGTATATCGAGCATATTTATATGAAGCCCATTACTTGAGCCCATATGGGCa                                                                                         <  2:777431/58‑1 (MQ=255)

                                                                                                                                  aTAGTATATCGAGCATATTTATATGAAGCCCATTACTTGAGCCCATATGGGCATATTTTTATAATGCAACTATTATGTAAACATTTATTTGTTATTTTGCTTTCTCCTGGAGGACACTCTTGACTGCTTTTGAGTAAAc   >  1:1351393/1‑139 (MQ=255)

                                                                                                                                   tAGTATATCGAGCATATTTATATGAAGCCCATTACTTGAGCCCAAATGGGCATATTTTTATAATGCAACTATTATGTAAACATTTATTTGTTATTTTGCTTTCTCCTGGAGGACACTCTTGACTGCTTTTGAGTAAACt  >  1:1142058/1‑139 (MQ=255)

GAAGGCGCTAAGCTGCTGAAATGTTCAGAGTTTGGTGAAGCGATCATCGAAAACATGTAATCTCTCCATGTGTTAAATATTGAAACGGGCGTATAACACGCCCGTTGTTTTATTTATGTGGATATTATTAATAGCATATCGAGCATATTTATATGAAGCCCATTACTTGAGCCCATATGGGCATATTTTTATAATGCAACTATTATGTAAACATTTATTTGTTATTTTGCTTTCTCCTGGAGGACACTCTTGACTGCTTTTGAGTAAACT  >  NC_000913/1211518‑1211787

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A