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
A9 F48 I1 R1	82	50.4	1709896	99.0%	1692797	139.8

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,614,131	G→T	L155L (CTG→CTT)	nikA →	Ni(2(+)) ABC transporter periplasmic binding protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,614,131	0	G	T	97.7%	147.4 / NA	44	L155L (CTG→CTT)	nikA	Ni(2(+)) ABC transporter periplasmic binding protein
Reads supporting (aligned to +/- strand): ref base G (0/0); major base T (19/24); minor base A (0/1); total (19/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TCCGCGCAGTGCTCGATAACCGTCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATTACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAGCGCCGATTGGCACCGGACCGTGGATTTTGCAGGAATCGAAACTGAATCAGTACG  >  NC_000913/3613995‑3614258

tCCGCGCAGTGCTCGATAACCGTCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATTACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTTGcc                                                                                                                              <  2:300839/140‑1 (MQ=255)

tCCCCGCAGTGCTCGATAGCCGTCATCGTCCCGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCGCTCAGTAAAACAGAGCTGCAAATTACCCTGAAAAGCGCCTACTTTCCTTTCCTGCAAGAACTAGcc                                                                                                                              <  2:760443/140‑1 (MQ=255)

            tCGATAACCGTCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATTTCCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTTGCCCTGCCCCGTCCt                                                                                                                  <  2:471293/140‑1 (MQ=255)

            tCGATAACCGTCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATTACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTTGCCCTGCCCCGTCCt                                                                                                                  <  1:502364/140‑1 (MQ=255)

            acGATAACCTCCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATTACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTTGCCCTGCCCCGTCCt                                                                                                                  <  2:286903/139‑1 (MQ=255)

              gATAACCGTCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATTACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTTGCCCTGCCCCGTCCttt                                                                                                                <  1:240545/140‑1 (MQ=255)

              gATAACCGTCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATTACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTTGCCCTGCCCCGTCCttt                                                                                                                <  1:598368/140‑1 (MQ=255)

                   ccGTCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATTACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTTGCCCTGCCCCGTCCTTTCCGtt                                                                                                           >  1:684233/1‑140 (MQ=255)

                         aCGTCACGCCTGGCTGGAGCTGGAAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATTACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTTGCCCTGCCCCGTCCTTTCCGTTTTATCg                                                                                                     <  1:332796/140‑1 (MQ=255)

                              aCGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATTACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTTGCCCTGCCCCGTCCTTTCCGTTTTATCGCTccc                                                                                                >  1:551511/1‑140 (MQ=255)

                                     gctggAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATTACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTTGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGt                                                                                         >  1:442323/1‑140 (MQ=255)

                                          aGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATTACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTTGCCCTGCCCCGTCCTTTCCGTTTTATCGCTccc                                                                                                <  2:336577/128‑1 (MQ=255)

                                          aGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATTACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTTGCCCTGCCCCGTCCTTTCCGTTTTATCGCTccc                                                                                                >  1:336577/1‑128 (MQ=255)

                                            cTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATTACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTTGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTaaaac                                                                                  >  2:275266/1‑139 (MQ=255)

                                             tGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATTACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTTGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAaaac                                                                                 <  2:658196/140‑1 (MQ=255)

                                               gCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATTACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTTGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAaaacca                                                                               >  2:382433/1‑140 (MQ=255)

                                               gCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATTAACCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTTGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAaaacca                                                                               >  2:190345/1‑140 (MQ=255)

                                                           tttgATGTTAAAGCACTCAGTAAAACAAAACTGCAAATTACCCTGAAAAGCGCCTACTAACCTTTCCTGCAAGAACTTGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAaccatgaaaccatgaa                                                                   <  2:580552/139‑1 (MQ=255)

                                                           gttgATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATTACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTTGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAaccatgaaaccatgaa                                                                   <  1:382433/140‑1 (MQ=255)

                                                           gttgATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATTACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTTGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAaccatgaaaccatgaa                                                                   <  1:740975/140‑1 (MQ=255)

                                                           gttgATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATTAACCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTTGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAaccatgaaaccatgaa                                                                   <  1:190345/140‑1 (MQ=255)

                                                                    aaaGCACTCAGTAAAACAGAGCTGCAAATTACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTTGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTaa                                                          >  1:301362/1‑140 (MQ=255)

                                                                      aGCACTCAGTAAAACAGAGCTGCAAATTACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTTGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAg                                                        >  1:208134/1‑140 (MQ=255)

                                                                           tCAGTAAAACAGAGCTGCAAATTACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTTGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAGCGCCg                                                   >  2:404216/1‑140 (MQ=255)

                                                                           tCAGTAAAACAGAGCTGCAAATTACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTTGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAGCGCCg                                                   >  1:255249/1‑140 (MQ=255)

                                                                            cAGTAAAACAGAGCTGCAAATTACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTTGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAGCGCCGa                                                  >  1:386863/1‑140 (MQ=255)

                                                                             aGTAAAACAGAGCTGCAAATTACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTTGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAGCGCCGAt                                                 <  2:813833/140‑1 (MQ=255)

                                                                             aGTAAAACAGAGCTGCAAATTACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTTGCCCTGCCCCGTCCTTTCCGTTTTATCGCTACCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAGCGCCGAt                                                 <  2:386863/140‑1 (MQ=255)

                                                                                       agCTGCAAATTACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTTGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAGCGCCGATTGGCACCggc                                       >  2:25023/1‑139 (MQ=255)

                                                                                       agCTGCAAATTACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTTGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAGCGCCGATTGGCACCGGa                                       >  2:629735/1‑140 (MQ=255)

                                                                                       agCTGCAAATTACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTTGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAGCGCCGATTGGCACCGGa                                       >  2:611615/1‑140 (MQ=255)

                                                                                         cTGCAAATTACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTTGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAGCGCCGATTGGCACCGGAcc                                     <  1:757427/140‑1 (MQ=255)

                                                                                         cTGCAAATTACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTTGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAGCGCCGATTGGCACCGGAcc                                     >  2:737233/1‑140 (MQ=255)

                                                                                                      tGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTTGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAGCGCCGATTGGCACCGGACCGTGGAt                               >  2:432986/1‑133 (MQ=255)

                                                                                                      tGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTTGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAGCGCCGATTGGCACCGGACCGTGGAt                               <  1:432986/133‑1 (MQ=255)

                                                                                                             cgcCTACTATCCTTTCCTGCAAGAACTTGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAGCGCCGATTGGCACCGGACCGTGGATTTTGCAGGAATCGa                 >  1:266670/1‑140 (MQ=255)

                                                                                                             cgcCTACTATCCTTTCCTGCAAGAACTTGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAGCGCCGATTGGCACCGGACCGTGGATTTTGCAGGAATCGa                 >  1:643888/1‑140 (MQ=255)

                                                                                                               ccaactaTCCTTTCCTGCAAGAACTTGCACTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAGCGCCGATTGGCACCGGACCTTGGATTTTGCAGGAATCGaaa               <  2:356427/137‑1 (MQ=255)

                                                                                                               ccTACTATCCTTTCCTGCAAGAACTTGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAGCGCCGATTGGCACCGGACCGTGGATTTTGCAGGAATCGaaa               <  2:208134/140‑1 (MQ=255)

                                                                                                                ctactaTCCTTTCCTGCAAGAACTTGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAGCGCCGATTGGCACCGGACCGTGGATTTTGCAGGAATCGAAAc              <  1:9749/140‑1 (MQ=255)

                                                                                                                      tCCTTTCCTGCAAGAACTTGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAGCGCCGATTGGCACCGGACCGTGGATTTTGCAGGAATCGAAACTGAATc        <  1:737233/140‑1 (MQ=255)

                                                                                                                      tCCTTTCCTGCAAGAACTTGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAGCGCCGATTGGCACCGGACCGTGGATTTTGCAGGAATCGAAACTGAATc        <  1:275266/140‑1 (MQ=255)

                                                                                                                           tCCTGCAAGACCTTGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGCAATTAAAGCGCCGATTGGCCCCGGACCGTGGATTTTGCAGGAATCGAAACT‑AATCAGTACg  <  2:446199/140‑1 (MQ=255)

                                                                                                                            ccTGCAAGAACTTGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAGCGCCGATTGGCACCGGACCGTGGATTTTGCAGGAATCGAAACTGAATCAGTACg  <  1:629735/140‑1 (MQ=255)

                                                                                                                            ccTGCAAGAACTTGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAGCGCCGATTGGCACCGGACCGTGGATTTTGCAGGAATCGAAACTGAATCAGTACg  <  1:404216/140‑1 (MQ=255)

TCCGCGCAGTGCTCGATAACCGTCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATTACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAGCGCCGATTGGCACCGGACCGTGGATTTTGCAGGAATCGAAACTGAATCAGTACG  >  NC_000913/3613995‑3614258

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 15 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A