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
A1 F169 I1 R1	62	44.4	970160	98.1%	951726	147.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	2,787,510	T→C	intergenic (+56/‑184)	zipA_3 → / → manR_2	Cell division protein ZipA/Transcriptional regulator ManR

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,787,510	0	T	C	100.0%	98.4 / NA	28	intergenic (+56/‑184)	zipA_3/manR_2	Cell division protein ZipA/Transcriptional regulator ManR
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (11/17); total (11/17)

AATAAATCAAATAATACCAATACGCCTTCTAAACAAACACCTCAAGCACAATCACCTAAAAATTAATCATTTGCCTGATACGTCCACAAGTACCAGATGCATAAATTCAGAAAAACAGCAGTGAGATATTTTTCTATTTGAAATATCTTACTGCTGTTCTTTATTTGCATAATTCGCACTCTGTTAAAATCATATAAAAGTTCGCTTTAATGTCATTGACGTATGTATAAGCTCTCAT  >  USA300TCH1516_ALE/2787389‑2787626

aataaATCAAATAATACCAATACGCCTTCTAAACAAACACCTCAAGCACAATCACCTAAAAATTAATCATTTGCCTGATACGTCCACAAGTACCAGATGCATAAATTCAGAAAAACAGCAGCGAGATATTTTTCTATTTGAAATATCt                                                                                            <  4:56116/148‑1 (MQ=255)

 ataaATCAAATAATACCAATACGCCTTCTAAACAAACACCTCAAGCACAATCACCTAAAAATTAATCATTTGCCTGATACGTCCACAAGTACCAGATGCATAAATTCAGAAAAACAGCAGCGAGATATTTTTCTATTTGAAATATCtt                                                                                           >  3:238162/1‑148 (MQ=255)

    aaTCAAATAATACCAATACGCCTTCTAAACAAACACCTCAAGCACAATCACCTAAAAATTAATCATTTGCCTGATACGTCCACAAGTACCAGATGCATAAATTCAGAAAAACAGCAGCGAGATATTTTTCTATTTGAAATATCTTAct                                                                                        <  3:54011/148‑1 (MQ=255)

      tCAAATAATACCAATACGCCTTCTAAACAAACACCTCAAGCACAATCACCTAAAAATTAATCATTTGCCTGATACGTCCACAAGTACCAGATGCATAAATTCAGAAAAACAGCAGCGAGATATTTTTCTATTTGAAATATCTTActgc                                                                                      >  4:74478/1‑148 (MQ=255)

           taataCCAATACGCCTTCTAAACAAACACCTCAAGCACAATCACCTAAAAATTAATCATTTGCCTGATACGTCCACAAGTACCAGATGCATAAATTCAGAAAAACAGCAGCGAGATATTTTTCTATTTGAAATATCTTACTGCTGTTc                                                                                 <  3:323319/148‑1 (MQ=255)

           taataCCAATACGCCTTCTAAACAAACACCTCAAGCACAATCACCTAAAAATTAATCATTTGCCTGATACGTCCACAAGTACCAGATGCATAAATTCAGAAAAACAGCAGCGAGATATTTTTCTATTTGAAATATCTTACTGCTGTTc                                                                                 <  3:198410/148‑1 (MQ=255)

            aataCCAATCCCCCTTCTAACCAACCCCCTCAAGCACAATCACCTAAAAATTAATCATTTGCCTGATACGTCCACAAGTACCAGATGCATAAATTCAGAAAAACAGCAGCGAGATATTTTTCTATTTGAAATATCTTActg                                                                                       <  2:25900/141‑1 (MQ=255)

            aataCCAATACGCCTTCTAAACAAACACCTCAAGCACAATCACCTAAAAATTAATCATTTGCCTGATACGTCCACAAGTACCAGATGCATAAATTCAGAAAAACAGCAGCGAGATATTTTTCTATTTGCAATATCTGActg                                                                                       <  1:48645/141‑1 (MQ=255)

             ataCCAATACGCCTTCTAAACAAACACCTCAAGCACAATCACCTAAAAATTAATCATTTGCCTGATACGTCCACAAGTACCAGATGCATAAATTCAGAAAAACAGCAGCGAGATATTTTTCTATTTGAAATATCTTActgc                                                                                      >  2:42550/1‑141 (MQ=255)

               aCCAATACGCCTTCTAAACAAACACCTCAAGCACAATCACCTAAAAATTAATCATTTGCCTGATACGTCCACAAGTACCAGATGCATAAATTCAGAAAAACAGCAGCGAGATATTTTTCTATTTGAAATATCTTActgctg                                                                                    >  2:3331/1‑141 (MQ=255)

               aCCAATACGCCTTCTAAACAAACACCTCAAGCACAATCACCTAAAAATTAATCATTTGCCTGATACGTCCACAAGTACCAGATGCATAAATTCAGAAAAACAGCAGCGAGATATTTTTCTATTTGAAATATCTTACTGCTGTTCTTTa                                                                             >  3:311093/1‑148 (MQ=255)

                 cAATACGCCTTCTAAACAAACACCTCAAGCACAATCACCTAAAAATTAATCATTTGCCTGATACGTCCACAAGTACCAGATGCATAAATTCAGAAAAACAGCAGCGAGATATTTTTCTATTTGAAATATCTTACTGCTGTTCTTTAtt                                                                           >  3:250936/1‑148 (MQ=255)

                           tCTAAACAAACACCTCAAGCACAATCACCTAAAAATTAATCATTTGCCTGATACGTCCACAAGTACCAGATGCATAAATTCAGAAAAACAGCAGCGAGATATTTTTCTATTTGAAATATCTTACTGCTGTTCTTTATTTGCATAATTc                                                                 >  4:66004/1‑148 (MQ=255)

                                           aaGCACAATCACCTAAAAATTAATCATTTGCCTGATACGTCCACAAGTACCAGATGCATAAATTCAGAAAAACAGCAGCGAGATATTTTTCTATTTGAAATATCTTACTGCTGTTCTTTATTTGCATAATTCGCACTCTGt                                                        <  1:54046/141‑1 (MQ=255)

                                              cacaATCACCTAAAAATTAATCATTTGCCTGATACGTCCACAAGTACCAGATGCATAAATTCAGAAAAACCGCAGCGAGATATTTTTCTATTTGAAATATCTTACTGCTGTTCTTTATTTGCATAATTCGCACTCTGTTAATATCata                                              <  4:354712/148‑1 (MQ=255)

                                                         aaataTTCATCAATTGCCCGACACGTCCACAAGTACCAGATGCATAAATTCAGAAAAACAGCAGCGAGATATTTTTCTATTTGAAATATCTTACTGCTGTTCTTTATTTGCATAATTCGCACTCTGTTAAAATCATATAAAAGTTCGc                                   <  4:129759/148‑1 (MQ=255)

                                                          aaaaTTAATCATTTGCCTGATACGTCCACAAGTACCAGATGCATAAATTCAGAAAAACAGCAGCGAGATATTTTTCTATTTGAAATATCTTACTGCTGTTCTTTATTTGCATAATTCGCACTCTGTTAAAATCATATAAAAGTTCGCt                                  >  4:208620/1‑148 (MQ=255)

                                                          aaaaTTAATCATTTGCCTGATACGTCCACAAGTACCAGATGCATAAATTCAGAAAAACAGCAGCGAGATATTTTTCTATTTGAAATATCTTACTGCTGTTCTTTATTTGCATAATTCGCACTCTGTTAAAATCATATAAAAGTTCGCt                                  <  4:270676/148‑1 (MQ=255)

                                                          aaaaTTAATCATTTGCCTGATACGTCCACAAGTACCAGATGCATAAATTCAGAAAAACAGCAGCGAGATATTTTTCTATTTGAAATATCTTACTGCTGTTCTTTATTTGCATAATTCGCACTCTGTTAAAATCATATAAAAGTTCGCt                                  >  4:46067/1‑148 (MQ=255)

                                                           aaaTTAATCATTTGCCTGATACGTCCACAAGTACCAGATGCATAAATTCAGAAAAACAGCAGCGAGATATTTTTCTATTTGAAATATCTTACTGCTGTTCTTTATTTGCATAATTCGCACTCTGTTAAAATCATATAAAAGTTCGCtt                                 <  3:339360/148‑1 (MQ=255)

                                                           aaaTTAATCATTTGCCTGATACGTCCACAAGTACCAGATGCATAAATTCAGAAAAACAGCAGCGAGATATTTTTCTATTTGAAATATCTTACTGCTGTTCTTTATTTGCATAATTCGCACTCTGTTAAAATCATATAAAAGTTCGCtt                                 <  4:53186/148‑1 (MQ=255)

                                                                        gCCTGATACGTCCACAAGTACCAGATGCATAAATTCAGAAAAACAGCAGCGAGATATTTTTCTATTTGAAATATCTTACTGCTGTTCTTTATTTGCATAATTCGCACTCTGTTAAAATCATATAAAAGTTCGCTTTAATGTCATTGAc                    <  3:172036/148‑1 (MQ=255)

                                                                           tGATACGTCCACAAGTACTATTTGCATAAATTCAGAAAAACAGCAGCGAGATATTTTTCTATTTGAAATATCTTACTGCTGTTCTTTATTTGCATAATTCGCACTCTGTTAAAATCATATAAAAGTTCGCTTTAATGTCATTGACgta                 <  3:22997/148‑1 (MQ=255)

                                                                           tGATACGTCCACAAGTACCAGATGCATAAATTCAGAAAAACAGCAGCGAGATATTTTTCTATTTGAAATATCTTACTGCTGTTCTTTATTTGCATAATTCGCACTCTGTTAAAATCATATAAAAGTTCGCTTTAATGTCATTGACgta                 <  4:196605/148‑1 (MQ=255)

                                                                             aTACGTCCACAAGTACCAGATGCATAAATTCAGAACAACAGCAGCGAGATATTTTTCTATTTGAAATATCTTACTGCTGTTCTTTATTTGCATAATTCGCACTCTGTTAAAATCATATAAAAGTTCGCTTTAATGTCATTGACgtatg               <  4:175080/148‑1 (MQ=255)

                                                                                 gTCCACAAGTACCAGATGCATAAATTCAGAAAAACAGCAGCGAGATATTTTTCTATTTGAAATATCTTACTGCTGTTCTTTATTTGCATAATTCGCACTCTGTTAAAATCATATAAAAGTTCGCTTTAATGTCATTGACGTATGtata           >  3:184676/1‑148 (MQ=255)

                                                                                 gTCCACAAGTACCAGATGCATAAATTCAGAAAAACAGCAGCGAGATATTTTTCTATTTGAAATATCTTACTGCTGTTCTTTATTTGCATAATTCGCACTCTGTTAAAATCATATAAAAGTTCGCTTTAATGTCATTGACGTATGtata           >  3:273617/1‑148 (MQ=255)

                                                                                          tACCAGATGCATAAATTCAGAAAAACAGCAGCGAGATATTTTTCTATTTGAAATATCTTACTGCTGTTCTTTATTTGCATAATTCGCACTCTGTTAAAATCATATAAAAGTTCGCTTTAATGTCATTGACGTATGTATAAGCTCTCAt  <  3:319508/148‑1 (MQ=255)

AATAAATCAAATAATACCAATACGCCTTCTAAACAAACACCTCAAGCACAATCACCTAAAAATTAATCATTTGCCTGATACGTCCACAAGTACCAGATGCATAAATTCAGAAAAACAGCAGTGAGATATTTTTCTATTTGAAATATCTTACTGCTGTTCTTTATTTGCATAATTCGCACTCTGTTAAAATCATATAAAAGTTCGCTTTAATGTCATTGACGTATGTATAAGCTCTCAT  >  USA300TCH1516_ALE/2787389‑2787626

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A