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	3,614,092	T→C	I142I (ATT→ATC)	nikA →	nickel/heme ABC transporter periplasmic binding protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,614,092	0	T	C	100.0%	140.3 / NA	40	I142I (ATT→ATC)	nikA	nickel/heme ABC transporter periplasmic binding protein
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (17/23); total (17/23)

GTTCGATGCCGAGGCGGCGGCAGAAAACTTCCGCGCAGTGCTCGATAACCGTCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATTACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAGCGCCGATTGGCACCGGAC  >  NC_000913/3613966‑3614222

gTTCGATGCCGAGGCGGCGGCAGAAAACTTCCGCGCAGTGCTCGATAACCGTCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAgc                                                                                                                        <  1:937142/139‑1 (MQ=255)

   cGATGCCGAGGCGGCGGCAGAAAACTTCCGCGCAGTGCTCGATAACCGTCAACGTCACGCCTGGCTGGAGCTGGCAGACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGcc                                                                                                                     <  2:456937/139‑1 (MQ=255)

   cGATGCCGAGGCGGCGGCAGAAAACTTCCGCGCAGTGCTCGATAACCGTCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGcc                                                                                                                     <  1:826842/139‑1 (MQ=255)

   cGATGCCGAGGCGGCGGCAGAAAACTTCCGCGCAGTGCTCGATAACCGTCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGcc                                                                                                                     <  1:231906/139‑1 (MQ=255)

                         aaCTTCCGCGCAGTGCTCGATAACCGTCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAAc                                                                                               <  1:132551/139‑1 (MQ=255)

                                        cTCGATAACCGTCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGaaa                                                                                                                           >  2:615843/1‑96 (MQ=255)

                                        cTCGATAACCGTCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGaaa                                                                                                                           <  1:615843/96‑1 (MQ=255)

                                            aTAACCGTCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCttt                                                                            <  2:958569/139‑1 (MQ=255)

                                                ccGTCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGt                                                                        >  1:1157296/1‑139 (MQ=255)

                                                  gTCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGttt                                                                      >  2:915904/1‑139 (MQ=255)

                                                         tCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCt                                                               <  1:324046/139‑1 (MQ=255)

                                                               ctggctggAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCg                                                         <  1:512615/139‑1 (MQ=255)

                                                                        gCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTaaa                                                <  2:1154233/139‑1 (MQ=255)

                                                                                               ttAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAAc                                                                                               >  2:598263/1‑69 (MQ=255)

                                                                                               ttAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAAc                                                                                               <  1:598263/69‑1 (MQ=255)

                                                                                                   aGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGc                                                        <  1:392786/104‑1 (MQ=255)

                                                                                                   aGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGc                                                        >  2:392786/1‑104 (MQ=255)

                                                                                                   aGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTaaa                     >  2:624981/1‑139 (MQ=255)

                                                                                                      aCTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAgcg                  >  1:304066/1‑139 (MQ=255)

                                                                                                        tCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAgcg                  >  2:1165622/1‑137 (MQ=255)

                                                                                                        tCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAgcg                  <  1:1165622/137‑1 (MQ=255)

                                                                                                              aaaCAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCa                                                                                                    >  2:255870/1‑49 (MQ=255)

                                                                                                              aaaCAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCa                                                                                                    <  1:255870/49‑1 (MQ=255)

                                                                                                               aaCAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGcc                                                                                          >  2:1023009/1‑58 (MQ=255)

                                                                                                               aaCAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGcc                                                                                          <  1:1023009/58‑1 (MQ=255)

                                                                                                                 cAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAGCGCCGATTGGCAc       <  2:379690/139‑1 (MQ=255)

                                                                                                                  agagCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAGCGCCGATTGGCAcc      <  2:1045162/139‑1 (MQ=255)

                                                                                                                    agCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAAc                                                                                               >  2:58517/1‑48 (MQ=255)

                                                                                                                    agCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAAc                                                                                               <  1:58517/48‑1 (MQ=255)

                                                                                                                    agCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGcc                                                                                          >  2:494374/1‑53 (MQ=255)

                                                                                                                    agCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGcc                                                                                          <  1:494374/53‑1 (MQ=255)

                                                                                                                    agCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGc                                                        <  2:16135/87‑1 (MQ=255)

                                                                                                                    agCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGc                                                        >  1:16135/1‑87 (MQ=255)

                                                                                                                      cTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCt                                                                              >  2:169632/1‑63 (MQ=255)

                                                                                                                      cTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCt                                                                              <  1:169632/63‑1 (MQ=255)

                                                                                                                      cTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAgcg                  <  2:361807/123‑1 (MQ=255)

                                                                                                                      cTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAgcg                  >  1:361807/1‑123 (MQ=255)

                                                                                                                      cTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAGCGCCGATTGGCACCGGAc  >  1:1139026/1‑139 (MQ=255)

                                                                                                                         cAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCa                                                       <  1:608893/83‑1 (MQ=255)

                                                                                                                         cAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCa                                                       >  2:608893/1‑83 (MQ=255)

GTTCGATGCCGAGGCGGCGGCAGAAAACTTCCGCGCAGTGCTCGATAACCGTCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATTACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAGCGCCGATTGGCACCGGAC  >  NC_000913/3613966‑3614222

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