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
A23 F110 I0 R1	32	23.2	500348	95.1%	475830	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	2,337,959	C→T	100%	intergenic (‑125/‑119)	USA300HOU_2195 ← / → USA300HOU_2196	possible MerR family transcriptional regulator/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	2,337,959	0	C	T	100.0%	95.0 / ‑6.5	32	intergenic (‑125/‑119)	USA300HOU_2195/USA300HOU_2196	possible MerR family transcriptional regulator/hypothetical protein
Reads supporting (aligned to +/- strand): ref base C (0/0); major base T (22/9); minor base A (1/0); total (23/9)
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TTTAGTTTTCATTGCGACTATCCTTTCAGTTATGTTTGGTCGTCTAAAGTAATGTTGCTTTATATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTACATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAGATTGATAATATTTAATTTTTTGAAAATTATTTTAGTTGCAATTTTTGGGTGATGCGGAAAATTTG  >  CP000730/2337823‑2338091

tttAGTTTTCATTGCGACTATCCTTTCAGTTATGTTTGGTCGTCTAAAGTAATGTTGCTTTATATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTATAttt                                                                                                                                  >  2:15202/1‑141 (MQ=255)

      tttCATTGCGACTATCCTTTCAGTTATGTTTGGTCGTCTAAAGTAATGTTGCTTTATATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTATATTTCATCGt                                                                                                                            >  2:31396/1‑141 (MQ=255)

        tCATTGCGACTATCATTTCAGTTATGTTTGGTCGTCTAAAGTAATGTTGCTTTATATATTGTCATCTTCGTTTGAATACTTATTATACATTCACGCAAATTTAAATTTGTCTCTTTTTTAACATTTTATATTTCATCGttt                                                                                                                          >  1:130712/1‑141 (MQ=255)

         cATTGCGACTATCCTTTCAGCACAGTGTGGTCGTCTAAAGTAATGTTGCTTTATATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTATATTTCATCGtttt                                                                                                                         >  1:247417/1‑141 (MQ=255)

             gCGACTATCCTTTCAGTTATGTTTGGTCGTCTAAAGTAATGTTGCTTTATATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTGATATTTCATCGTTTTTAAt                                                                                                                     >  1:9151/1‑141 (MQ=255)

              cGACTATCCTTTCAGTTATGTTTGGTCGTCTAAAGTAATGTTGCTTTATATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTATATTTCATCGTTTTTAAtt                                                                                                                    >  1:37114/1‑141 (MQ=255)

              cGACTATCCTTTCAGATATGTTTGGTCGTCTAAAGTAATGTTGATTTATATATTGTCATCTTCGTTTGAATACTTCTTGTTTTATTACTCATATTTAAATTTGTCTCTTTTTTAACATTTTATCTTTCATCGTTTTTAttt                                                                                                                    >  2:94153/1‑141 (MQ=255)

              cGACTATCCTGTCAGTTATGTTGGGTCGTCTAAAGTAATGTTGCTTTATATATTGTCATCGTCGTTTGAATACTTCTTATTTTCATAATCAAAATTAAATGTAGCTCTTCTTTTACCTTTTCAAATTCATTGTTTTTTAtt                                                                                                                    >  2:38737/1‑141 (MQ=255)

                 cTATCCTTTCATTTATGTTTGGTCGTCTAAAGTAATGTTGCTTTATATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTCCTCAAATTTAAATTTGTCTCTTTTTTAACATTTTATATTTCATCGTTTTTAATTACt                                                                                                                 <  1:36870/141‑1 (MQ=255)

                 cTATCCTTTCAGTTATGTTTGGTCGTCTAAAGTAATGTTGCTTTATATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTATATTTCATCGTTTTTAATTACt                                                                                                                 <  1:33737/141‑1 (MQ=255)

                              tATGTTTGGTCGTCTAAAGTAATGTTGCTTTATATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTATCTTTCATCGTTTTTAATTACTTTAACAATTGtat                                                                                                    >  2:50402/1‑141 (MQ=255)

                                   ttGGTCGTCTAAAGTAATGTTGCTTTATATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACtt                                                                                               >  1:118572/1‑141 (MQ=255)

                                    tGGTCGTCTAAAGTAATGTTGCTTAATATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTa                                                                                              >  1:159551/1‑141 (MQ=255)

                                       tcgtcTAAAGTAATGTTTCTTTATATATTGTAATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAat                                                                                           <  2:39621/141‑1 (MQ=255)

                                             aaaGTAATGTTGCTTTATATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTaa                                                                                     >  2:138768/1‑141 (MQ=255)

                                                       tGCTTTATATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATaa                                                                           >  2:40583/1‑141 (MQ=255)

                                                              tatatTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTaa                                                                    >  1:104219/1‑141 (MQ=255)

                                                                      cATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAGATTGata                                                            >  2:88899/1‑141 (MQ=255)

                                                                         tttCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAGATTGataata                                                         <  2:169178/140‑1 (MQ=255)

                                                                         cTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAGATTGataata                                                         <  1:72304/141‑1 (MQ=255)

                                                                             gTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAGATTGATAATATTTa                                                     >  2:246607/1‑141 (MQ=255)

                                                                                   aTACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTATTATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTTACATTGATAATATTTAAttttt                                               >  2:119261/1‑141 (MQ=255)

                                                                                   aTACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAGATTGATAATATTTAAttttt                                               >  2:133104/1‑141 (MQ=255)

                                                                                      cttcttATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAGATTGATAATATTTAATTTTTTGa                                            >  1:216916/1‑141 (MQ=255)

                                                                                                 attaCTCAAATTTAAATTTGTCTCTTTTTTAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAGATTGATAATATTTAATTTTTTGAAAATTATTTTa                                 <  2:159551/141‑1 (MQ=255)

                                                                                                             taaatttGTCTCTTTTTTAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAGATTGATAATATTTAATTTTTTGAAAATTATTTTTGTTGCAAttttt                     >  1:215816/1‑141 (MQ=255)

                                                                                                                   tGTCTCTTTTTTAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAGATTGATAATATTTAATTTTTTGAAAATTATTTTAGTTGCAATTTTTGGGTGa               <  1:88899/141‑1 (MQ=255)

                                                                                                                          tttttAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAGATTGATAATATTTAATTTTTTGAAAATTATTTTAGTTGCAATTTTTGGGTGATGCGGaa        <  1:18769/141‑1 (MQ=255)

                                                                                                                             ttAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAGATTGATAATATTTAATTTTTTGAAAATTCTTTTAGTTGCAATTTTTGGGTGATGCGGaaatt     >  2:47057/1‑139 (MQ=255)

                                                                                                                              tAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAGATTGATAATATTTAATTTTTTGAAAATTATTTTAGTTGCAATTTTTGGGTGATGCGGAAAAtt    >  2:70298/1‑141 (MQ=255)

                                                                                                                                aCATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAGATTGATAATATTTAATTTTTTGAAAATTATTTTAGTTGCAATTTTTGGGTGATGCGGAAAATTTg  <  2:216916/141‑1 (MQ=255)

                                                                                                                                aCATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAGATTGATAATATTTAATTTTTTGAAAATTATTTTAGTTGCAATTTTTGGGTGATGCGGAAAATTTg  >  1:196159/1‑141 (MQ=255)

TTTAGTTTTCATTGCGACTATCCTTTCAGTTATGTTTGGTCGTCTAAAGTAATGTTGCTTTATATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTACATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATGATATAATCACTAAGATTGATAATATTTAATTTTTTGAAAATTATTTTAGTTGCAATTTTTGGGTGATGCGGAAAATTTG  >  CP000730/2337823‑2338091

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A