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 F1 I1 R1	770	51.4	2439994	93.8%	2288714	110.3

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%	114.3 / NA	32	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 (15/17); total (15/17)

ATGCGGTACCAGAAGAACAGGTTGATCCGCGCAAAGCGGCAGTTGCCGCGGCTATTGCCCGCGCTCAGGCCAAAAAAGCCGCCCAGCAGAAGGTTGTAAACGAGGACTAAATGGTATTCAGAATAGCTAGCTCCCCTTATACCCATAACCAGCGCCAGACATCGCGCATTATGCTGTTGGTGTTGCTCGCAGCCGTGCCAGGAATCGCAGCGCAACTGTGGTTTTTTGGTTGGGGTACTCTCGTTCAGATCCTGTTGGCATCG  >  NC_000913/1709032‑1709294

aTGCGGTACCAGAAGAACAGGTTGATCCGCGCAAAGCGGCAGTTGCCGCGGCTATTGCCCGCGCTCAGGCCAAAAAAGCCGCCCAGCAGAAGGTTGTAAACGAGGACTAAATGGTATTCAGAATAGCTAGCCCCCCTta                                                                                                                              >  1:851469/1‑139 (MQ=255)

   cGGTACCAGAAGAACAGGTTGATCCGCGCAAAGCGGCAGTTGCCGCGGCTATTGCCCGCGCTCAGGCCAAAAAAGCCGCCCAGCAGAAGGTTGTAAACGAGGACTAAATGGTATTCAGAATAGCTAGCCCCCCTTATAc                                                                                                                           >  1:197930/1‑139 (MQ=255)

          agaagaACAGGTTGATCCGCGCAAAGCGGCAGTTGCCGCGGCTATTGCCCGCGCTCAGGCCAAAAAAGCCGCCCAGCAGAAGGTTGTAAACGAGGACTAAATGGTATTCAGAATAGCTAGCCCCCCTTATACCCATAAc                                                                                                                    <  1:752808/139‑1 (MQ=255)

             agaaCAGGTTGATCCGCGCAAAGCGGCAGTTGCCGCGGCTATTGCCCGCGCTCAGGCCAAAAAAGCCGCCCAGCAGAAGGTTGTAAACGAGGACTAAATGGTATTCAGAATAGCTAGCCCCCCTTATACCCATAAc                                                                                                                    <  2:372287/136‑1 (MQ=255)

             agaaCAGGTTGATCCGCGCAAAGCGGCAGTTGCCGCGGCTATTGCCCGCGCTCAGGCCAAAAAAGCCGCCCAGCAGAAGGTTGTAAACGAGGACTAAATGGTATTCAGAATAGCTAGCCCCCCTTATACCCATAAc                                                                                                                    >  1:372287/1‑136 (MQ=255)

                aCAGGTTGATCCGCGCAAAGCGGCAGTTGCCGCGGCTATTGCCCGCGCTCAGGCCAAAAAAGCCGCCCAGCAGAAGGTTGTAAACGAGGACTAAATGGTATTCAGAATAGCTAGCCCCCCTTATACCCATAACCAgcgc                                                                                                              <  1:1183346/139‑1 (MQ=255)

                  aGGTTGATCCGCGCAAAGCGGCAGTTGCCGCGGCTATTGCCCGCGCTCAGGCCAAAAAAGCCGCCCAGCAGAAGGTTGTAAACGAGGACTAAATGGTATTCAGAATAGCTAGCCCCCCTTATACCCATAACCAGCGCCa                                                                                                            <  2:165220/139‑1 (MQ=255)

                    gTTGATCCGCGCAAAGCGGCAGTTGCCGCGGCTATTGCCCGCGCTCAGGCCAAAAAAGCCGCCCAGCAGAAGGTTGTAAACGAGGACTAAATGGTATTCAGAATAGCTAGCCCCCCTTATACCCATAACCAGCGCCAGa                                                                                                          >  1:86172/1‑139 (MQ=255)

                         tCCGCGCAAAGCGGCAGTTGCAGCGGCTATTGCCCGCGCTCAGGCCAAAAAAGCCGCCCAGCAGAAGGTTGTAAACGAGGACTAAATGGAATTCAGAATAGCTAGCCCCCCTTATACCCATAACCAGCGCCAGACATcg                                                                                                     >  1:733616/1‑139 (MQ=255)

                             cgcAAAGCGGCAGTTGCCGCGGCTATTGCCCGCGCTCAGGCCAAAAAAGCCGCCCAGCAGAAGGTTGTAAACGAGGACTAAATGGTATTCAGAATAGCTAGCCCCCCTTATACCCATAACCAGCGCCAGACATCGCGCa                                                                                                 >  1:754091/1‑139 (MQ=255)

                                   gCGGCAGTTGCCGCGGCTATTGCCCGCGCTCAGGCCAAAAAAGCCGCCCAGCAGAAGGTTGTAAACGAGGACTAAATGGTATTCAGAATAGCTAGCCCCCCTTATACCCATAACCAGCGCCAGACATCGCGCATTATGc                                                                                           <  2:197930/139‑1 (MQ=255)

                                           tGCCGCGGCTATTGCCCGCGCTCAGGCCAAAAAAGCCGCCCAGCAGAAGGTTGTAAACGAGGACTAAATGGTATTCAGAATAGCTAGCCCCCCTTATACCGATAACCAGCGCCAGACATCGCGCATTATGCTGTTGgtg                                                                                   <  2:250618/139‑1 (MQ=255)

                                                             cgcTCAGGCCAAAAAAGCCGCCCAGCAGAAGGTTGTAAACGAGGACTAAATGGTATTCAGAATAGCTAGCCCCCCTTATACCCATAACCAGCGCCAGACATCGCGCATTATGCTGTTGGTGTTGCTCGCAGCCGTGCCa                                                                 >  1:1070182/1‑139 (MQ=255)

                                                                   ggCCAAAAAAGCCGCCCAGCAGAAGGTTGTAAACGAGGACTAAATGGTATTCAGAATAGCTAGCCCCCCTTATACCCATAACCAGCGCCAGACATCGCGCATTATGCTGTTGgtg                                                                                   <  2:449527/115‑1 (MQ=255)

                                                                   ggCCAAAAAAGCCGCCCAGCAGAAGGTTGTAAACGAGGACTAAATGGTATTCAGAATAGCTAGCCCCCCTTATACCCATAACCAGCGCCAGACATCGCGCATTATGCTGTTGgtg                                                                                   >  1:449527/1‑115 (MQ=255)

                                                                       aaaaaaGCCGCCCAGCAGAAGGTTGTAAACGAGGACTAAATGGTATTCAGAATAGCTAGCCCCCCTTATACCCATAACCAGCGCCAGACATCGCGCATTATGCTGTTGGTGTTGCTCGCAGCCGTGCCAGGAATCGCAg                                                       <  1:99541/139‑1 (MQ=255)

                                                                       aaaaaaGCCGCCCAGCAGAAGGTTGTAAACGAGGACTAAATGGTATTCAGAATAGCTAGCCCCCCTTATACCCATAACCAGCGCCAGACATCGCGCATTATGCTGTTGGTGTTGCTCGCAGCCGTGCCAGGAATCGCAg                                                       <  2:1070182/139‑1 (MQ=255)

                                                                                              tGTAAACGAGGACTAAATGGTATTCAGAATAGCTAGCCCCCCTta                                                                                                                              <  2:984050/45‑1 (MQ=255)

                                                                                              tGTAAACGAGGACTAAATGGTATTCAGAATAGCTAGCCCCCCTta                                                                                                                              >  1:984050/1‑45 (MQ=255)

                                                                                              tGTAAACGAGGACTAAATGGTATTCAGAATAGCTAGCCCCCCTTATACCCATAACCAGCGCCAGACATCGCGCATTATGCTGTTGGTGTTGCTCGCAGCCGTGCCAGGAATCGCAGCGCAACTGTGGTTTTttggt                                   <  1:585576/136‑1 (MQ=255)

                                                                                              tGTAAACGAGGACTAAATGGTATTCAGAATAGCTAGCCCCCCTTATACCCATAACCAGCGCCAGACATCGCGCATTATGCTGTTGGTGTTGCTCGCAGCCGTGCCAGGAATCGCAGCGCAACTGTGGTTTTttggt                                   >  2:585576/1‑136 (MQ=255)

                                                                                                tAAACGAGGACTAAATGGTATTCAGAATAGCTAGCCCCCCTTATACCCATAACCAGCGCCAGACATCGCGCATTATGCTGTTGGTGTTGCTCGCAGCCGTGCCAGGAATCGCAGCGCAACTGTGGTTTTTTGGTTgggg                              <  2:235363/139‑1 (MQ=255)

                                                                                                        gACTAAATGGTATTCAGAATAGCTAGCCCCCCTTATACCCATAACCAGCGCCAGACATCGCGCATTATGCTGTTGGTGTTGCTCGCAGCCGTGCCAGGAATCGCAGCGCAACTGTGGttt                                         >  1:332579/1‑120 (MQ=255)

                                                                                                        gACTAAATGGTATTCAGAATAGCTAGCCCCCCTTATACCCATAACCAGCGCCAGACATCGCGCATTATGCTGTTGGTGTTGCTCGCAGCCGTGCCAGGAATCGCAGCGCAACTGTGGttt                                         <  2:332579/120‑1 (MQ=255)

                                                                                                          cTAAATGGTATTCAGAATAGCTAGCCCCCCTTATACCCATAACCa                                                                                                                  >  1:527808/1‑45 (MQ=255)

                                                                                                          cTAAATGGTATTCAGAATAGCTAGCCCCCCTTATACCCATAACCa                                                                                                                  <  2:527808/45‑1 (MQ=255)

                                                                                                          cTAAATGGTATTCAGAATAGCTAGCCCCCCTTATACCCATAACCAGCGCCAGACATCGCGCATTATGCTGTTGGTGTTGCTCGCAGCCGTGCCAGGAATCGCAGCGCAACTGTGGTTTTTTGGTTGGGGTACTCTCGtt                    <  1:639394/139‑1 (MQ=255)

                                                                                                                  tATTCAGAATAGCTAGCCCCCCTTATACCCATAACCAGCGCCAGACATCGCGCATTATGCTGTTGGTGTTGCTCGCAg                                                                         >  1:744404/1‑78 (MQ=255)

                                                                                                                  tATTCAGAATAGCTAGCCCCCCTTATACCCATAACCAGCGCCAGACATCGCGCATTATGCTGTTGGTGTTGCTCGCAg                                                                         <  2:744404/78‑1 (MQ=255)

                                                                                                                   aTTCAGAATAGCTAGCCCCCCTTATACCCATAACCAGCGCCAGACATCGCGCAtt                                                                                               <  2:303008/55‑1 (MQ=255)

                                                                                                                   aTTCAGAATAGCTAGCCCCCCTTATACCCATAACCAGCGCCAGACATCGCGCAtt                                                                                               >  1:303008/1‑55 (MQ=255)

                                                                                                                       aGAATAGCTAGCCCCCCTTATACCCATAACCAGCGCCAGACATCGCGCATTATGCTGTTGGTGTTGCTCGCAGCCGTGCCAGGAATCGCAGCGCAACTGTGGTTTTTTGGTTGGGGTACTCTCGTTCAGATCCTGTTgg       >  2:487009/1‑139 (MQ=255)

                                                                                                                            agctagccCCCCTTATACCCATAACCAGCGCCAGACATCGCGCATTATGCTGTTGGTGTTGCTCGCAGCCGTGCCAGGAATCGCAGCGCAACTGTGGTTTTTTGGTTGGGGTACTCTCGTTCAGATCCTGTTGGCATCg  >  1:572071/1‑139 (MQ=255)

                                                                                                                              ctagccCCCCTTATACCCATAACCAGCGCCAGACATCGCGCATTATGCTGTTGGTGTTGCTCGCAGCCGTGCCAGGAATCGCAGCGCAACTGTGGtttttt                                      <  1:561694/101‑1 (MQ=255)

                                                                                                                              ctagccCCCCTTATACCCATAACCAGCGCCAGACATCGCGCATTATGCTGTTGGTGTTGCTCGCAGCCGTGCCAGGAATCGCAGCGCAACTGTGGtttttt                                      >  2:561694/1‑101 (MQ=255)

ATGCGGTACCAGAAGAACAGGTTGATCCGCGCAAAGCGGCAGTTGCCGCGGCTATTGCCCGCGCTCAGGCCAAAAAAGCCGCCCAGCAGAAGGTTGTAAACGAGGACTAAATGGTATTCAGAATAGCTAGCTCCCCTTATACCCATAACCAGCGCCAGACATCGCGCATTATGCTGTTGGTGTTGCTCGCAGCCGTGCCAGGAATCGCAGCGCAACTGTGGTTTTTTGGTTGGGGTACTCTCGTTCAGATCCTGTTGGCATCG  >  NC_000913/1709032‑1709294

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A