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 I0 R1	75	34.0	794130	95.7%	759982	140.9

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	96.6%	92.1 / ‑4.4	29	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 (11/17); minor base T (1/0); total (12/17)
Fisher's exact test for biased strand distribution p-value = 4.14e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.61e-01
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.

TTGATAAGGGAAGATTTACCAGCACCATTCGGGCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAATGTATGTGAGGTGAAAGTATGTTAACTGAAGAA  >  USA300TCH1516_ALE/707773‑708045

ttGATAAGGGAAGATTTACCAGCACCATTCGGGCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGt                                                                                                                                      <  1:45415/141‑1 (MQ=255)

    tAAGGGAAGATTTACCAGCACCATTCGGGCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTtat                                                                                                                                  >  2:186255/1‑141 (MQ=255)

     aaGGGAAGATTTACCAGCACCATTCGGGCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTtata                                                                                                                                 >  2:320557/1‑141 (MQ=255)

             aTTTACCAGCACCATTCGGGCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTaa                                                                                                                         <  1:126188/141‑1 (MQ=255)

                tACCAGCACCATTCGGGCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGCTAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTa                                                                                                                      >  1:122027/1‑141 (MQ=255)

                 aCCAGCACCATTCGGGCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTaa                                                                                                                     <  1:64560/141‑1 (MQ=255)

                        ccATTCGGGCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTa                                                                                                              <  1:345477/141‑1 (MQ=255)

                           ttCGGGCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGc                                                                                                           >  2:328675/1‑141 (MQ=255)

                                gCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAAcc                                                                                                      <  2:207942/141‑1 (MQ=255)

                                               tattTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTataa                                                                                       >  1:331932/1‑141 (MQ=255)

                                                        gcgTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTgag                                                                              <  2:16139/141‑1 (MQ=255)

                                                            aCTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAATCAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAGGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAata                                                                          >  2:167732/1‑141 (MQ=255)

                                                                            agaTGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTa                                                          <  2:41248/139‑1 (MQ=255)

                                                                              cggtgtttAAGTACATGCCGATTAGCTAAATACAGGTGTAAATCGTTTGTTGCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTTACATGTCAAGTaaa                                                        >  2:392609/6‑141 (MQ=255)

                                                                               tGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAAt                                                       >  2:46046/1‑141 (MQ=255)

                                                                               tGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATATATCGAAAGTGTTTATAGTTTAAATCATCTAAGAAAAAGTTTAGGCTAACTTAAATAATTGTATGATAAACTGAGAATATTTATCATGTCAAGTAAAt                                                       >  1:189949/1‑141 (MQ=255)

                                                                                      aaGTACATGCCTATTACCAAAAAACAGTTTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCCAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGat                                                <  1:190908/141‑1 (MQ=255)

                                                                                           cATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGatataat                                           <  1:320557/141‑1 (MQ=255)

                                                                                                     aCCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAatg                                 >  1:174538/1‑141 (MQ=255)

                                                                                                          aaaaCAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATCTATCATGTCAAGTAACTTCGTGATATAATATAGACAatgtatgt                            <  2:350322/141‑1 (MQ=255)

                                                                                                          aaaaCAGATTTAAATCTTTTGTTTCTAACAAGCGTTGATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAatgtatgt                            <  1:30170/141‑1 (MQ=255)

                                                                                                          aaaaCAGATTTAAATCTTTTGGTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAatgtatgt                            <  1:14032/141‑1 (MQ=255)

                                                                                                             aCAGATTTAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGCTATACTATAGACAATGTATGTGAg                         >  2:126833/1‑141 (MQ=255)

                                                                                                                    tAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTGAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAATGTATGTGAGGTGAAAg                  <  1:88785/141‑1 (MQ=255)

                                                                                                                    tAAATCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAATGTATGTGAGGTGAAAg                  <  1:125540/141‑1 (MQ=255)

                                                                                                                        tCTTTTGTTTCTAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAATGTATGTGAGGTGAAAGTATg              <  1:46046/141‑1 (MQ=255)

                                                                                                                                 tcgaaCAAGCGTTTAGACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAATGTATGTGAGGTGAAAGTATGTTAACTgaa     <  1:346862/138‑1 (MQ=255)

                                                                                                                                   tAACAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAATGTATGTGAGGTGAAAGTATGTTAACTgaaga   >  1:107117/1‑141 (MQ=255)

                                                                                                                                    aaCAAGCGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAATGTATGTGAGGTGAAAGTATGTTAACTgaagaa  <  2:56677/141‑1 (MQ=255)

TTGATAAGGGAAGATTTACCAGCACCATTCGGGCCCATGATACCAATTATTTCGCCGCGTACTGGTATCGATAAGGAAATGTTTTTAAGTACATGCTTATTACCTAAAAACAGATTTAAATCTTTTGTTTCTAACAAACGTTTATACCTCCTAATTAAAAGTTTAGGCTAACCTAATTAATTGTATAATAAACTGAGAATATTTATCATGTCAAGTAAATTCGTGATATAATATAGACAATGTATGTGAGGTGAAAGTATGTTAACTGAAGAA  >  USA300TCH1516_ALE/707773‑708045

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A