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 F1 I1 R1	773	79.9	4112934	92.2%	3792125	104.5

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,709,163	T→C	S8P (TCC→CCC)	rsxD →	SoxR iron‑sulfur cluster reduction factor component, putative membrane protein of electron transport complex

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,709,163	0	T	C	100.0%	92.7 / NA	27	S8P (TCC→CCC)	rsxD	SoxR iron‑sulfur cluster reduction factor component, putative membrane protein of electron transport complex
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (15/12); total (15/12)

CAGGTTGATCCGCGCAAAGCGGCAGTTGCCGCGGCTATTGCCCGCGCTCAGGCCAAAAAAGCCGCCCAGCAGAAGGTTGTAAACGAGGACTAAATGGTATTCAGAATAGCTAGCTCCCCTTATACCCATAACCAGCGCCAGACATCGCGCATTATGCTGTTGGTGTTGCTCGCAGCCGTGCCAGGAATCGCAGCGCAACTGTGGTTTTTTGGTTGGGGTACTCTCGTTCAGATCCTGTTGGCATCGGT  >  NC_000913/1709049‑1709296

cAGGTTGATCCGCGCAAAGCGGCAGTTGCCGCGGCTATTGCCCGCGCTCAGGCCAAAAAAGCCGCCCAGCAGAAGGTTGTAAACGAGGACTAAATGGTATTCAGAATAGCTAGCCCCCCTTATACCCATAACCAGCGcc                                                                                                               >  2:641771/1‑139 (MQ=255)

  ggTTGATCCGCGCAAAGCGGCAGTTGCCGCGGCTATTGCCCGCGCTCAGGCCAAAAAAGCCGCCCAGCAGAAGGTTGTAAACGAGGACTAAATGGTATTCAGAATAGCTAGCCCCCCTTATACCCATAACCAGCGCCAg                                                                                                             >  2:491902/1‑139 (MQ=255)

       aTCCGCGCAAAGCGGCAGTTGCCGCGGCTATTGCCCGCGCTCAGGCCAAAAAAGCCGCCCAGCAGAAGGTTGTAAACGAGGACTAAATGGTATTCAGAATAGCTAGCCCCCCTTATACCCATAACCAGCGCCAGACATc                                                                                                        <  1:491902/139‑1 (MQ=255)

             gcAAAGCGGCAGTTGCCGCGGCTATTGCCCGCGCTCAGGCCAAAAAAGCCGCCCAGCAGAAGGTTGTAAACGAGGACTAAATGGTATTCAGAATAGCTAGCCCCCCTTATACCCATAACCAGCGCCAGACATCGCGCAt                                                                                                  >  2:1907749/1‑139 (MQ=255)

                                    aTTGCCCGCGCACAGGCCAAAAAAGCCGCCCAGCAGAAGGTTGTAAACGAGGACTAAATGGTATTCAGAATAGCTAGCCCCCCTTATACCCATAACCAGCGCCAGACATCGCGCATTATGCTGTTGGTGTTGCTCGCAg                                                                           <  2:1332800/139‑1 (MQ=255)

                                           gcgcTCAGGCCAAAAAAGCCGCCCAGCAGAAGGTTGTAAACGAGGACTAAATGGTATTCAGAATAGCTAGCCCCCCTTATACCCATAAc                                                                                                                      <  2:656118/89‑1 (MQ=255)

                                           gcgcTCAGGCCAAAAAAGCCGCCCAGCAGAAGGTTGTAAACGAGGACTAAATGGTATTCAGAATAGCTAGCCCCCCTTATACCCATAAc                                                                                                                      >  1:656118/1‑89 (MQ=255)

                                            cgcTCAGGCCAAAAAAGCCGCCCAGCAGAAGGTTGTAAACGAGGACTAAATGGTATTCAGAATAGCTAGCCCCCCTTATACCCATAACCAGCGCCAGACATCGCGCATTATGCTGTTGGTGtt                                                                                   <  2:797714/123‑1 (MQ=255)

                                            cgcTCAGGCCAAAAAAGCCGCCCAGCAGAAGGTTGTAAACGAGGACTAAATGGTATTCAGAATAGCTAGCCCCCCTTATACCCATAACCAGCGCCAGACATCGCGCATTATGCTGTTGGTGtt                                                                                   >  1:797714/1‑123 (MQ=255)

                                                 aGGCCAAAAAAGCCGCCCAGCAGAAGGTTGTAAACGAGGACTAAATGGTATTCAGAATAGCTAGCCCCCCTTATACCCATAACCAGCGCCAGACATCGCGCATTATGCTGTTGGTGTTGCTCGCAGCCGTGCCAGGAAt                                                              <  1:1907749/139‑1 (MQ=255)

                                                 aGGCCAAAAAAGCCGCCCAGCAGAAGGTTGTAAACGAGGACTAAATGGTATTCAGAATAGCTAGCCCCCCTTATACCCATAACCAGCGCCAGACATCGCGCATTATGCTGTTGGTGTTGCTCGCAGCCGTGCCAGGAAt                                                              <  1:641771/139‑1 (MQ=255)

                                                                                    gAGGACTAAATGGTATTCAGAATAGCTAGCCCCCCTTATACCCATAACCAGCGCCAGACATCGCGCATTATGCTGTTGGTGTTGCTCGCAGCCGTGCCAGGAATCGCAGCGCAACTGTGGTTTTTTGGTTGGGGTActc                           >  2:1244696/1‑139 (MQ=255)

                                                                                     aGGACTAAATGGTATTCAGAATAGCTAGCCCCCCTTATACCCATAACCAGCGCCAGACATCGCGCATTATGCTGTTGGTGTTGCTCGCAGCCGTGCCAGGAATCGCAGCGCAACTGTGGTTTTTTGGTTGGGGTActct                          >  2:1996141/1‑139 (MQ=255)

                                                                                      ggACTAAATGGTATTCAGAATAGCTAGCCCCCCTTATACCCATAAc                                                                                                                      >  2:1350802/1‑46 (MQ=255)

                                                                                      ggACTAAATGGTATTCAGAATAGCTAGCCCCCCTTATACCCATAAc                                                                                                                      <  1:1350802/46‑1 (MQ=255)

                                                                                      ggACTAAATGGTATTCAGAATAGCTAGCCCCCCTTATACCCATAACCAGCGCCAGACATCGCGCATTATGCTGTTGGTGTTGCTCGCAGCCGTGCCAGGAATCGCAGCGCAACTGTGGTTTTTTGGTTGGGGTACtctc                         >  2:1373285/1‑139 (MQ=255)

                                                                                         cTAAATGGTATTCAGAATAGCTAGCCCCCCTTATACCCATAACCa                                                                                                                    >  2:823296/1‑45 (MQ=255)

                                                                                         cTAAATGGTATTCAGAATAGCTAGCCCCCCTTATACCCATAACCa                                                                                                                    <  1:823296/45‑1 (MQ=255)

                                                                                               ggTATTCAGAATAGCTAGCCCCCCTTATACCCATAACCAGCGCCAGACATCGCGCATTATGCTGTTGGTGTTGCTCGCAGCCGTGCCAGGAATCGCAGCGCAACTGTGGTTTTTTGGTTGGGGTActct                          <  1:492077/129‑1 (MQ=255)

                                                                                               ggTATTCAGAATAGCTAGCCCCCCTTATACCCATAACCAGCGCCAGACATCGCGCATTATGCTGTTGGTGTTGCTCGCAGCCGTGCCAGGAATCGCAGCGCAACTGTGGTTTTTTGGTTGGGGTActct                          >  2:492077/1‑129 (MQ=255)

                                                                                                 tATTCAGAATAGCTAGCCCCCCTTATACCCATAACCAGCGCCAGACATCGCGCATTATGCTGTTGGTGTTGCTCGCAGCCGTGCCAGGAAt                                                              >  2:221854/1‑91 (MQ=255)

                                                                                                 tATTCAGAATAGCTAGCCCCCCTTATACCCATAACCAGCGCCAGACATCGCGCATTATGCTGTTGGTGTTGCTCGCAGCCGTGCCAGGAAt                                                              <  1:221854/91‑1 (MQ=255)

                                                                                                        aaTAGCTAGCCCCCCTTATACCCATAACCAGCGCCAGACATCGCGCa                                                                                                   <  1:536315/47‑1 (MQ=255)

                                                                                                        aaTAGCTAGCCCCCCTTATACCCATAACCAGCGCCAGACATCGCGCa                                                                                                   >  2:536315/1‑47 (MQ=255)

                                                                                                        aaTAGCTAGCCCCCCTTATACCCATAACCAGCGCCAGACATCGCGCATTATGCTGTTGGTGTTGCTCGCAg                                                                           >  2:1863219/1‑71 (MQ=255)

                                                                                                        aaTAGCTAGCCCCCCTTATACCCATAACCAGCGCCAGACATCGCGCATTATGCTGTTGGTGTTGCTCGCAg                                                                           <  1:1863219/71‑1 (MQ=255)

                                                                                                        aaTAGCTAGCCCCCCTTATACCCATAACCAGCGCCAGACATCGCACATTATGCTGTTGGTGTTGCTCGCAGCCGTGCCAGGAATCGCAGCGCAACTGTGGTTTTTTGGTTGGGGTACTCTCGTTCAGATCCTGTTGGCa       >  1:1454365/1‑139 (MQ=255)

                                                                                                             ctagccCCCCTTATACCCATAACCAGCGCCAGACATCGCGCATTATGCTGTTGGTGTTGCTCGCAGCCGTTCCAGGAATCGCAGCGCAACTGTGGTTTTTTGGTTGGGGTACTCTCGTTCAGATCCTGTTGGCATCGGt  >  1:528429/1‑139 (MQ=255)

                                                                                                             ctagccCCCCTTATACCCATAACCAGCGCCAGACATCGCGCATTATGCTGTTGGTGTTGCTCGCAGCCGTGCCAGGAATCGCAGCGCAACTGTGGTTTTTTGGTTGGGGTActct                          <  1:712190/115‑1 (MQ=255)

                                                                                                             ctagccCCCCTTATACCCATAACCAGCGCCAGACATCGCGCATTATGCTGTTGGTGTTGCTCGCAGCCGTGCCAGGAATCGCAGCGCAACTGTGGTTTTTTGGTTGGGGTActct                          >  2:712190/1‑115 (MQ=255)

                                                                                                             ctagccCCCCTTATACCCATAACCAGCGCCAGACATCGCGCATTATGCTGTTGGTGTTGCTCGCAGCCGTGCCAGGAATCGCAGCGCAACTGTGGTTTTTTGGTTGGGGTACTCTCGTTCAGATCCTGTTGGCATCGGt  <  2:1504223/139‑1 (MQ=255)

                                                                                                             ctagccCCCCTTATACCCATAACCAGCGCCAGACATCGCGCATTATGCTGTTGGTGTTGCTCGCAGCCGTGCCAGGAATCGCAGCGCAACTGTGGTTTTTTGGTTGGGGTACTCTCGTTCAGATCCTGTTGGCATCGGt  >  1:1504223/1‑139 (MQ=255)

                                                                                                             ctagccCCCCTTATACCCATAACCAGCGCCAGACATCGCGCATTATGCTGTTGGTGTTGCTCGCAGCCGTGCCAGGAATCGCAGCGCAACTGTGGTTTTTTGGTTGGGGTACTCTCGTTCAGATCCTGTTGGCATCGGt  <  1:1373285/139‑1 (MQ=255)

CAGGTTGATCCGCGCAAAGCGGCAGTTGCCGCGGCTATTGCCCGCGCTCAGGCCAAAAAAGCCGCCCAGCAGAAGGTTGTAAACGAGGACTAAATGGTATTCAGAATAGCTAGCTCCCCTTATACCCATAACCAGCGCCAGACATCGCGCATTATGCTGTTGGTGTTGCTCGCAGCCGTGCCAGGAATCGCAGCGCAACTGTGGTTTTTTGGTTGGGGTACTCTCGTTCAGATCCTGTTGGCATCGGT  >  NC_000913/1709049‑1709296

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A