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
A6 F1 I1 R1	750	51.0	2595496	93.6%	2429384	106.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,769,648	(C)_6→5	intergenic (+162/‑55)	yfjQ → / → yfjR	CP4‑57 prophage, uncharacterized protein/CP4‑57 prophage, putative DNA‑binding transcriptional regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,769,643	0	C	.	100.0%	108.8 / NA	27	intergenic (+157/‑60)	yfjQ/yfjR	CP4‑57 prophage, uncharacterized protein/CP4‑57 prophage, putative DNA‑binding transcriptional regulator
Reads supporting (aligned to +/- strand): ref base C (0/0); new base . (13/14); total (13/14)

TTAATATCGGACACCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATCAGCCGTCTGGTTGCGGGT  >  NC_000913/2769508‑2769777

ttAATATCGGACACCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGcccc                                                                                                                                     <  1:397405/139‑1 (MQ=255)

       cGGACACCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTa                                                                                                                             <  1:80663/139‑1 (MQ=255)

                ccTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATca                                                                                                                    >  1:183936/1‑139 (MQ=255)

                   gTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATCAcat                                                                                                                 <  1:460105/139‑1 (MQ=255)

                          tCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCCTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTtc                                                                                                          <  2:94157/139‑1 (MQ=255)

                              tATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTtcagtc                                                                                                      <  1:585385/139‑1 (MQ=255)

                                        tgtgCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACttt                                                                                            <  2:981930/139‑1 (MQ=255)

                                               cAATCCCCCGTGTATAGCTTTTAACCCCCGTTACAGCTGGCGTTTGCAGGAATAAAAGATAGTTTCTGCGTTGTCCATACCCTGGCCG‑CCCCCGCTGTAAAGTAATCACTTCATTTTCAGTCAGTTAACTTTCCTGgag                                                                                     >  2:630000/1‑139 (MQ=18)

                                               cAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGgag                                                                                     >  2:1061035/1‑139 (MQ=255)

                                                   cccccGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAAtc                                                                                 <  1:1061035/139‑1 (MQ=255)

                                                            ataGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTaa                                                                                                <  2:995775/115‑1 (MQ=255)

                                                            ataGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTaa                                                                                                >  1:995775/1‑115 (MQ=255)

                                                                   ttAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATCAcat                                                                                                                 >  1:1121630/1‑91 (MQ=255)

                                                                   ttAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATCAcat                                                                                                                 <  2:1121630/91‑1 (MQ=255)

                                                                    tAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCAt                                                                           >  1:514410/1‑128 (MQ=255)

                                                                    tAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCAt                                                                           <  2:514410/128‑1 (MQ=255)

                                                                    tAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAg                                                                >  1:577405/1‑139 (MQ=255)

                                                                    tAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAg                                                                >  1:851966/1‑139 (MQ=255)

                                                                       cccccGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAAc                                                             <  2:577405/139‑1 (MQ=255)

                                                                          ccGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTtcagt                                                                                                       >  1:481549/1‑94 (MQ=255)

                                                                          ccGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTtcagt                                                                                                       <  2:481549/94‑1 (MQ=255)

                                                                                      gCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGcccc                                                                                                                                     >  1:820869/1‑53 (MQ=255)

                                                                                      gCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGcccc                                                                                                                                     <  2:820869/53‑1 (MQ=255)

                                                                                      gCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCggc                                              >  2:282731/1‑139 (MQ=255)

                                                                                       cTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGcccc                                                                                                                                     <  2:551362/52‑1 (MQ=255)

                                                                                       cTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGcccc                                                                                                                                     >  1:551362/1‑52 (MQ=255)

                                                                                           tGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGcccc                                                                                                                                     >  2:459033/1‑48 (MQ=255)

                                                                                           tGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGcccc                                                                                                                                     <  1:459033/48‑1 (MQ=255)

                                                                                                 aaTAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTggctgtcagg                                   <  2:851966/139‑1 (MQ=255)

                                                                                                               tCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCa                                                                            >  1:989861/1‑84 (MQ=255)

                                                                                                               tCTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCa                                                                            <  2:989861/84‑1 (MQ=255)

                                                                                                                cTGCGTTGTCCATACCCTGTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATc                    <  1:202950/139‑1 (MQ=255)

                                                                                                                                  gTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATCAGCCGTCTGGTTGCGGGt  >  1:267868/1‑139 (MQ=255)

                                                                                                                                  gTCCG‑CCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATCAGCCGTCTGGTTGCGGGt  >  1:1257703/1‑139 (MQ=255)

TTAATATCGGACACCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCCCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATCAGCCGTCTGGTTGCGGGT  >  NC_000913/2769508‑2769777

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A