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
A5 F178 I0 R1	41	49.4	1100758	95.6%	1052324	140.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	707,910	A→G	100%	intergenic (‑1/‑121)	znuC_1 ← / → ideR	High‑affinity zinc uptake system ATP‑binding protein ZnuC/Iron‑dependent repressor IdeR

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	707,910	0	A	G	100.0%	120.6 / ‑6.5	41	intergenic (‑1/‑121)	znuC_1/ideR	High‑affinity zinc uptake system ATP‑binding protein ZnuC/Iron‑dependent repressor IdeR
Reads supporting (aligned to +/- strand): ref base A (0/0); major base G (18/22); minor base T (1/0); total (19/22)
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.

GATAAGGGAAGATTTACCAGCACCATTCGGGCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAATGTATGTGAGGTGAAAGTATGTTAACTGAAGA  >  USA300TCH1516_ALE/707775‑708044

tgcaaGGGAAGTGTTACCTGCACCAGTCGCGCCCATGCTACTCATTATGTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGtt                                                                                                                                    <  2:511390/137‑1 (MQ=255)

tattaGGGAAGATTTACCACCACCATTCGGGCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGtt                                                                                                                                    <  2:209050/136‑1 (MQ=255)

       gAAGATTTACCAGCACCATTCGGGCCCATGATACCAATTCTTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATAcct                                                                                                                             >  1:190439/1‑140 (MQ=255)

         aGATTTACCAGCACCATTCGGGCCCATGACACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATAcctcc                                                                                                                           >  2:196738/1‑140 (MQ=255)

             ttACCAGCACCATTCGGGCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAAt                                                                                                                       <  2:538206/140‑1 (MQ=255)

                ccAGCACCATTCGGGCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGATTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTaa                                                                                                                    >  1:99489/1‑140 (MQ=255)

                            gggCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAATCGTTTATACCTCCTATTTAAAATTTTAGGCTa                                                                                                        >  1:243765/1‑140 (MQ=255)

                                cgagtgtACCTATTATTTCGCCGCGTTCTGCTATCGATAAGGATATGTTTTTAAGTACATGCTTATTACCTAAAACCACATTCACATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAATGTTTAGGCTAACCt                                                                                                    <  2:79090/134‑1 (MQ=255)

                                ccATGATACCAATTATTTCGCCGCTTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAACAGTTTAGGCTAACCt                                                                                                    <  1:490265/140‑1 (MQ=255)

                                ccATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCt                                                                                                    <  1:398274/140‑1 (MQ=255)

                                ccATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCt                                                                                                    >  1:149205/1‑140 (MQ=255)

                                ccATGACACCAAGTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCt                                                                                                    <  2:149269/140‑1 (MQ=255)

                                  aTGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCtaa                                                                                                  >  1:135919/1‑140 (MQ=255)

                                  aTGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAAATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTTGGCTAACCtaa                                                                                                  >  1:308222/1‑140 (MQ=255)

                                   tGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAACAGTTTAGGCTAACCtaat                                                                                                 <  2:488439/140‑1 (MQ=255)

                                     aTACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCtaatta                                                                                               >  2:485043/1‑140 (MQ=255)

                                     aTACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATAACTCCTAATTAAAAGTTTAGGCTAACCtaatta                                                                                               >  1:64456/1‑140 (MQ=255)

                                         cAATTATTTCTCCGAGTACTGGTATCGATAAGGAAATTTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTg                                                                                           <  1:272164/140‑1 (MQ=255)

                                                              gTATCGCTAAGGAAATGTTTTTAATTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGACTAACCTAATTAATTGTAGAATAAACTGAGAATAttt                                                                      >  1:351161/1‑140 (MQ=255)

                                                                     tAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTTTTTCCAACAAGCGTTTATACCTCCTAATTAAAAATTTAAGATAACTAAATTAAATGATTAATAAACTGAGAATATTTATCATGt                                                               >  1:176769/1‑140 (MQ=255)

                                                                     tAAGGAAATGTAGTTAAATACATGCTGAGTACCTAAAAACAGATTTAAATCGTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGt                                                               >  2:543873/1‑140 (MQ=255)

                                                                      aaGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTc                                                              >  2:79467/1‑140 (MQ=255)

                                                                           aaTTTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTa                                                         <  2:6645/140‑1 (MQ=255)

                                                                           aaTGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTGATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTa                                                         <  1:517911/140‑1 (MQ=255)

                                                                           aaTGTTTGTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTa                                                         <  2:111767/140‑1 (MQ=255)

                                                                                  ttAAGTACATGCTTATTACCTAAAAACGGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGt                                                  <  1:382591/140‑1 (MQ=255)

                                                                                  ttAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTCCAGTGTCCAATGACAAAATAAACTGCTCCTTTTTATCATGTCAAGTAAATTCGt                                                  >  1:124443/1‑140 (MQ=255)

                                                                                            gCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTTCTTATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGatataatat                                        <  1:291430/140‑1 (MQ=255)

                                                                                                  taCCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACaa                                  <  2:111496/140‑1 (MQ=255)

                                                                                                   acgtAAAAACAGATTTAAATCTTTTGTCTCTAACAAGCGTTTATTCTTCCTAATTAAAAGTTTATTCTAATCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAat                                 <  1:21802/137‑1 (MQ=255)

                                                                                                     cTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAatgt                               >  1:252346/1‑140 (MQ=255)

                                                                                                      tAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAatgta                              >  1:232324/1‑140 (MQ=255)

                                                                                                            cAGATTTAAATCTTTTGTTTCTAATAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAATCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAATGTATGTGAg                        <  1:216659/140‑1 (MQ=255)

                                                                                                                tttAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAGCTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAATGTATGTGAGGTGa                    >  1:370873/1‑140 (MQ=255)

                                                                                                                 atAAATCTTTTGTTTCTAACAAGCATTTATACCTCCTAATTAAAGGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAAATCGAGCTATAATATAGGCAATGTAGGAGAGGCGaa                   >  2:169823/2‑140 (MQ=255)

                                                                                                                           tGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAAATCGTGATATAATATAGACAATATATATGAGGTGAAAGTATGTTaa         >  1:389193/1‑140 (MQ=255)

                                                                                                                            ttttCTAACAAGCGTTTATACATTCTAATTAAAAGGTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAATGTATGTGAGGTGAAAGTATGTTAAc        <  1:249715/139‑1 (MQ=255)

                                                                                                                             tttCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAATGTATGTGAGGTGAAAGTATGTTAACt       <  2:99489/140‑1 (MQ=255)

                                                                                                                                  aaCAAGCGTTTATACCTCCTAATTAAAAGTTTATGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAATGTATGTGAGGTGAAAGTATGTTAACTgaaga  <  2:308222/140‑1 (MQ=255)

                                                                                                                                  aaCAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAATGTATGTGAGGTGAAAGTATGTTAACTgaaga  <  2:135919/140‑1 (MQ=255)

                                                                                                                                  aaCAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAATGTATGTGAGGTGAAAGTATGTTAACTgaaga  <  1:532543/140‑1 (MQ=255)

GATAAGGGAAGATTTACCAGCACCATTCGGGCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAATGTATGTGAGGTGAAAGTATGTTAACTGAAGA  >  USA300TCH1516_ALE/707775‑708044

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A