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
A4 F1 I1 R1	765	39.6	1867486	94.4%	1762906	108.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,128,134	C→T	T99M (ACG→ATG)	murJ →	putative lipid II flippase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,128,134	0	C	T	100.0%	122.4 / NA	39	T99M (ACG→ATG)	murJ	putative lipid II flippase
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (18/21); total (18/21)

TTTGCCGAAGGGGCATTTTCCCAGGCATTTGTACCGATTCTGGCGGAATATAAAAGTAAGCAGGGTGAAGACGCCACGCGGGTCTTTGTCTCTTATGTTTCTGGCCTGCTGACACTTGCGCTGGCGGTTGTGACGGTCGCTGGCATGCTCGCCGCACCGTGGGTGATCATGGTGACCGCGCCAGGCTTCGCTGACACAGCTGACAAATTTGCCCTGACCAGCCAGCTACTAAAGATTACCTTTCCCTATATCTTGCTGATCTCC  >  NC_000913/1128001‑1128264

tttGCCGAAGGGGCATTTTCCCAGGCATTTGTACCGATTCTGGCGGAATATAAAAGTAAGCAGGGTGAAGACGCCACGCGGGTCTTTGTCTCTTATGTTTCTGGCCTGCTGACACTTGCGCTGGCGGTTGTGATGGTCg                                                                                                                               <  2:339497/139‑1 (MQ=255)

       aaGGGGCATTTTCCCAGGCATTTGTACCGATTCTGGCGGAATATAAAAGTAAGCAGGGTGAAGACGCCACGCGGGTCTTTGTCTCTTATGTTTCTGGCCTGCTGACACTTGCGCTGGCGGTTGTGATGGTCGCTGGCAt                                                                                                                        >  2:240177/1‑139 (MQ=255)

       aaGGGGCATTTTCCCAGGCATTTGTACCGATTCTGGCGGAATATAAAAGTAAGCAGGGTGAAGACGCCACGCGGGTCTTTGTCTCTTATGTTTCTGGCCTGCTGACACTTGCGCTGGCGGTTGTGATGGTCGCTGGCAt                                                                                                                        <  1:348497/139‑1 (MQ=255)

                  tCCCAGGCATTTGTACCGATTCTGGCGGAATATAAAAGTAAGCAGGGTGAAGACGCCACGCGGGTCTTTGTCTCTTATGTTTCTGGCCTGCTGACACTTGCGCTGGCGGTTGTGATGGTCGCTGGCATGCTCGCCGCAc                                                                                                             <  1:413583/139‑1 (MQ=255)

                   cccAGGCATTTGTACCGATTCTGGCGGAATATAAAAGTAAGCAGGGTGAAGACGCCACGCGGGTCTTTGTCTCTTATGTTTCTGGCCTGCTGACACTTGCGCTGGCGGTTGTGATGGTCGCTGGCATGCTCGCCGCa                                                                                                              >  1:154997/1‑137 (MQ=255)

                   cccAGGCATTTGTACCGATTCTGGCGGAATATAAAAGTAAGCAGGGTGAAGACGCCACGCGGGTCTTTGTCTCTTATGTTTCTGGCCTGCTGACACTTGCGCTGGCGGTTGTGATGGTCGCTGGCATGCTCGCCGCa                                                                                                              <  2:154997/137‑1 (MQ=255)

                          aTTTGTACCGATTCTGGCGGAATATAAAAGTAAGCAGGGTGAAGACGCCACGCGGGTCTTTGTCTCTTATGTTTCTGGCCTGCTGACACTTGCGCTGGCGGTTGTGATGGTCGCTGGCATGCTCGCCGCACCGTGGGTg                                                                                                     <  2:548773/139‑1 (MQ=255)

                            ttGTACCGATTCTGGCGGAATATAAAAGTAAGCAGGGTGAAGACGCCACGCGGGTCTTTGTCTCTTATGTTTCTGGCCTGCTGACACTTGCGCTGGCGGTTGTGATGGTCGCTGGCATGCTCGCCGCAc                                                                                                             <  1:415934/129‑1 (MQ=255)

                            ttGTACCGATTCTGGCGGAATATAAAAGTAAGCAGGGTGAAGACGCCACGCGGGTCTTTGTCTCTTATGTTTCTGGCCTGCTGACACTTGCGCTGGCGGTTGTGATGGTCGCTGGCATGCTCGCCGCAc                                                                                                             >  2:415934/1‑129 (MQ=255)

                                                        tAAGCAGGGTGAAGACGCCACGCGGGTCTTTGTCTCTTATGTTTCTGGCCTGCTGACACTTGCGCTGGCGGTTGTGATGGt                                                                                                                                 <  2:786103/81‑1 (MQ=255)

                                                        tAAGCAGGGTGAAGACGCCACGCGGGTCTTTGTCTCTTATGTTTCTGGCCTGCTGACACTTGCGCTGGCGGTTGTGATGGt                                                                                                                                 >  1:786103/1‑81 (MQ=255)

                                                        tAAGCAGGGTGAAGACGCCACGCGGGTCTTTGTCTCTTATGTTTCTGGCCTGCTGACACTTGCGCTGGCGGTTGTGATGGTCGCTGGCATGCTCGCCGCACCGTGGGTGATCATGGTGACCGCGCCAGGc                                                                                >  2:564145/1‑130 (MQ=255)

                                                        tAAGCAGGGTGAAGACGCCACGCGGGTCTTTGTCTCTTATGTTTCTGGCCTGCTGACACTTGCGCTGGCGGTTGTGATGGTCGCTGGCATGCTCGCCGCACCGTGGGTGATCATGGTGACCGCGCCAGGc                                                                                <  1:564145/130‑1 (MQ=255)

                                                          aGCAGGGTGAAGACGCCACGCGGGTCTTTGTCTCTTATGTTTCTGGCCTGCTGACACTTGCGCTGGCGGTTGTGATGGTCGCTGGCATGCTCGCCGCACCGTGGGTGATCATGGTGACCGCGCCAGGCTTCGCTGacac                                                                     >  2:837381/1‑139 (MQ=255)

                                                                     gACGCCACGCGGGTCTTTGTCTCTTATGTTTCTGGCCTGCTGACACTTGCGCTGGCGGTTGTGATGGTCGCTGGCATGCTCGCCGCACCGTGGGTGATCATGGTGACCGCGCCAGGCTTCGCTGACACAGCTGACAAAt                                                          <  1:240177/139‑1 (MQ=255)

                                                                         ccACGCGGGTCTTTGTCTCTTATGTTTCTGGCCTGCTGACACTTGCGCTGGCGGTTGTGATGGTCGCTGGCATGCTCGCCGCACCGTGGGTGATCATGGTGACCGCGCCAGGCTTCGCTGACACAGCTGACAAATTTGc                                                      >  2:134660/1‑139 (MQ=255)

                                                                                  tCTTTGTCTCTTATGTTTCTGGCCTGCTGACACTTGCGGTGGCGGTTGTGATGGTCAGTAGCATGCTCGCCGCAACGAAGGTGATCATGGTGACCGCGCCAGGCTTCGCTGACAGACCTGACAAATTTGCCCTGGccag                                             >  2:305832/1‑139 (MQ=255)

                                                                                    tttGTCTCTTATGTTTCTGGCCTGCTGACACTTGCGCTGGCGGTTGTGATGGTCGCTGGCATGCTCGCCGCACCGTGGGTGATCATGGTGACCGCGCCAGGCTTCGCTGACACAGCTGACAAATTTGcc                                                     <  1:297261/129‑1 (MQ=255)

                                                                                    tttGTCTCTTATGTTTCTGGCCTGCTGACACTTGCGCTGGCGGTTGTGATGGTCGCTGGCATGCTCGCCGCACCGTGGGTGATCATGGTGACCGCGCCAGGCTTCGCTGACACAGCTGACAAATTTGcc                                                     >  2:297261/1‑129 (MQ=255)

                                                                                       gTCTCTTATGTTTCTGGCCTGCTGACACTTGCGCTGGCGGTTGTGATGGTCGCTGGCATGCTCGCCGCACCGTggg                                                                                                       <  1:423343/76‑1 (MQ=255)

                                                                                       gTCTCTTATGTTTCTGGCCTGCTGACACTTGCGCTGGCGGTTGTGATGGTCGCTGGCATGCTCGCCGCACCGTggg                                                                                                       >  2:423343/1‑76 (MQ=255)

                                                                                                     tGGCCTGCTGACACTTGCGCTGGCGGTTGTGATGGTCGCTGGCATGCTCGCCGCACCGTGGGTGATCATGGTGACCGCGCCAGGCTTCGCTGACACAGCTGACAAATTTGCCCTGACCAGCCAGCTACTAAAGATTAcc                          <  1:134660/139‑1 (MQ=255)

                                                                                                      ggCCTGCTGACACTTGCGCTGGCGGTTGTGATGGTCGCTGGCATGCTCGCCGCACCGTGGGTGATCATGGTGACCGCGCCAGGCTTCGCTGACACAGCTGACAAATTTGCCCTGAccag                                             <  1:218430/119‑1 (MQ=255)

                                                                                                      ggCCTGCTGACACTTGCGCTGGCGGTTGTGATGGTCGCTGGCATGCTCGCCGCACCGTGGGTGATCATGGTGACCGCGCCAGGCTTCGCTGACACAGCTGACAAATTTGCCCTGAccag                                             >  2:218430/1‑119 (MQ=255)

                                                                                                            ctgACACTTGCGCTGGCGGTTGTGATGGTCGCTGGCATGCTCGCCGCACCGt                                                                                                          >  2:556197/1‑52 (MQ=255)

                                                                                                            ctgACACTTGCGCTGGCGGTTGTGATGGTCGCTGGCATGCTCGCCGCACCGt                                                                                                          <  1:556197/52‑1 (MQ=255)

                                                                                                            ctgACACTTGCGCTGGCGGTTGTGATGGTCGCTGGCATGCTCGCCGCACCGTGGGTGATCATGGTGACCGCGCCAGGCTTCGCTGACACAGCTGACAAATTTGcc                                                     <  2:15585/105‑1 (MQ=255)

                                                                                                            ctgACACTTGCGCTGGCGGTTGTGATGGTCGCTGGCATGCTCGCCGCACCGTGGGTGATCATGGTGACCGCGCCAGGCTTCGCTGACACAGCTGACAAATTTGcc                                                     >  1:15585/1‑105 (MQ=255)

                                                                                                            ctgACACTTGCGCTGGCGGTTGTGATGGTCGCTGGCATGCTCGCCGCACCGTGGGTGATCATGGTGACCGCGCCAGGCTTCGCTGACACAGCTGACAAATTTGCCCTGACCAGCCAGCTACTAAAGATTACCTTTCCCt                   <  1:837381/139‑1 (MQ=255)

                                                                                                            ctgACACTTGCGCTGGCGGTTGTGATGGTCGCTGGCATGCTCGCCGCACCGTGGGTGATCATGGTGACCGCGCCAGGCTTCGCTGACACAGCTGACAAATTTGCCCTGACCAGCCAGCTACTAAAGATTACCTTTCCCt                   <  2:795889/139‑1 (MQ=255)

                                                                                                                    tGCGCTGGCGGTTGTGATGGTCGCTGGCATGCTCGCCGCACCGTGGGTGATCATGGTGACCGCGCCAGGCTTCGCTGACACAGCTGACAAATTTGCCCTGACCAGCCAGCTACTAAAGATTAcc                          >  2:471650/1‑124 (MQ=255)

                                                                                                                    tGCGCTGGCGGTTGTGATGGTCGCTGGCATGCTCGCCGCACCGTGGGTGATCATGGTGACCGCGCCAGGCTTCGCTGACACAGCTGACAAATTTGCCCTGACCAGCCAGCTACTAAAGATTAcc                          <  1:471650/124‑1 (MQ=255)

                                                                                                                      cgcTGGCGGTTGTGATGGTCGCTGGCATGCTCGCCGCACCGTGGGTGATCATGGTGACCGCGCCAGGCTTCGCTGACACAg                                                                   >  2:511298/1‑81 (MQ=255)

                                                                                                                      cgcTGGCGGTTGTGATGGTCGCTGGCATGCTCGCCGCACCGTGGGTGATCATGGTGACCGCGCCAGGCTTCGCTGACACAg                                                                   <  1:511298/81‑1 (MQ=255)

                                                                                                                      cgcTGGCGGTTGTGATGGTCGCTGGCATGCTCGCCGCACCGTGGGTGATCATGGTGACCGCGCCAGGCTTCGCTGACACAGCTGACAAATTTGcc                                                     >  1:517735/1‑95 (MQ=255)

                                                                                                                      cgcTGGCGGTTGTGATGGTCGCTGGCATGCTCGCCGCACCGTGGGTGATCATGGTGACCGCGCCAGGCTTCGCTGACACAGCTGACAAATTTGcc                                                     <  2:517735/95‑1 (MQ=255)

                                                                                                                        cTGGCGGTTGTGATGGTCGCTGGCATGCTCGCCGCACCGTGGGTGATCATGGTGACCGCGCCAGGCTTCGCTGACACAGCTGACAAATTTGCCCTGACCAGCCAGCTACTAAAGATTACCTTTCCCTATATCTTGCTGa       >  2:257533/1‑139 (MQ=255)

                                                                                                                                 gtgATGGTCGCTGGCATGCTCGCCGCACCGTGGGTGATCATGGTGACCGCGCCAGGCTTCGCTGACACAGCTGACAAATTTGCCCTGACCAGCCAGCTACTAAAGATTACCTTTCCCTATATCTTGCTGATCTcc  >  2:31702/1‑135 (MQ=255)

                                                                                                                                 gtgATGGTCGCTGGCATGCTCGCCGCACCGTGGGTGATCATGGTGACCGCGCCAGGCTTCGCTGACACAGCTGACAAATTTGCCCTGACCAGCCAGCTACTAAAGATTACCTTTCCCTATATCTTGCTGATCTcc  <  1:31702/135‑1 (MQ=255)

TTTGCCGAAGGGGCATTTTCCCAGGCATTTGTACCGATTCTGGCGGAATATAAAAGTAAGCAGGGTGAAGACGCCACGCGGGTCTTTGTCTCTTATGTTTCTGGCCTGCTGACACTTGCGCTGGCGGTTGTGACGGTCGCTGGCATGCTCGCCGCACCGTGGGTGATCATGGTGACCGCGCCAGGCTTCGCTGACACAGCTGACAAATTTGCCCTGACCAGCCAGCTACTAAAGATTACCTTTCCCTATATCTTGCTGATCTCC  >  NC_000913/1128001‑1128264

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A