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
A4 F13 I0 R1	140	52.5	2164708	98.8%	2138731	146.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947_CJ‑RC	4,158,466	T→G	56.4%	L159R (CTG→CGG)	PP_3661 →	membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947_CJ‑RC	4,158,466	0	T	G	56.4%	‑4.6 / 9.5	27	L159R (CTG→CGG)	PP_3661	membrane protein
Reads supporting (aligned to +/- strand): ref base T (4/7); new base G (10/5); total (15/12)
Fisher's exact test for biased strand distribution p-value = 2.33e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.57e-01

TGCTGGTAGTCACCAGTACCCTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCTGCGCAGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCATCTGGATACCATGGGCGCCGGGCTGCTGCTGGGCGGCA  >  NC_002947_CJ‑RC/4158325‑4158609

tGCTGGTAGTCACCAGTACCCTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCggcgcggcgcc                                                                                                                                            >  2:84774/1‑146 (MQ=255)

      tAGTCACCAGTACCCTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCTGCGCACCGccc                                                                                                                                      >  6:202802/1‑147 (MQ=255)

          cACCAGTACCCTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGGGCGGGGCGCCGcccccc                                                                                                                                   >  3:88085/1‑146 (MQ=255)

            ccAGTACCCTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCGGCGCAGCGccccccca                                                                                                                                 >  2:94847/1‑144 (MQ=255)

            ccAGTACCCTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGAGGCGCACccccccccca                                                                                                                                 >  1:178047/1‑144 (MQ=255)

             cAGTACCCTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCAGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGGGCGGGCCCCCGcccccccaa                                                                                                                                >  1:249623/1‑143 (MQ=255)

              aGTACCCTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCGGCGCCGCGcccccccaaa                                                                                                                               >  6:14317/1‑142 (MQ=255)

                                      tgtggCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGGGGGGCGCCGCCCCCCCCAAAAAAAACCCAGGGGAGTCGGGAgaggt                                                                                                      >  7:239457/1‑143 (MQ=255)

                                        tggCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCGGCGCACCCCCCCCCAAAAAAACGCCAAGGCAGTCGGGAGCGTAga                                                                                                    >  2:42939/1‑146 (MQ=255)

                                           cATTAATGTTTTCAAGCTCGAGGGCTATCCCGCGTTGCTGACCGCCGCCGGCTGCGCCTTTTGCGGCGCCGCCGCGGGGCGGTAATTCTATTCGGCGGTGCGCTGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGc                                                                                                  <  2:14334/146‑1 (MQ=255)

                                             tGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCGGGGCCGCCCCCCCCAAAAAAGCCCCAAGGCACTAGGGACCGGAGTGATGt                                                                                               >  6:213926/1‑147 (MQ=255)

                                                 cgggtTCACGCTCGCCCGCTAACCCGCGGTGCTCCCGGCCGCCGGCCCCGCCAGCGGGGGCGCCGCCGCGGGGGGGGCTTTCTACGCGGCGCGGCGCAGCGCCCCCCATAAACGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCgg                                                                                           <  2:107021/144‑1 (MQ=255)

                                                              gACGGCTATACCGCCTTGCTGACCGCCGCCGTCAGCGCCATCTGGGGCGCCGCCGCGGTGCTGTAATTCTAATCGGCGCTGCGCAGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATg                                                                              <  8:134895/147‑1 (MQ=255)

                                                                                 tgcccgccgccgGCAGCGCCATCGGCGGCGCCGCCGCGGGGCTGCCATTCCAAGCGGCGCTGCGCAGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGa                                                           <  2:115318/144‑1 (MQ=255)

                                                                                 tccccggcgcggGCTGCGCATTCTGGGGGGCCGCCGCGGTGCTGGAATTCTTTTCGGCGCTGGGCTGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGa                                                           <  4:8860/144‑1 (MQ=255)

                                                                                                gcgcCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCAGCGCAGCGCCCCCCAAAAAAACGCCATGGCAGTCGGAAGCGTATTGCTGTTCGGTAACATGTCGATTTTACATTTACCACAGGCGCTAAATGCCagcaggc                                            >  6:254872/1‑147 (MQ=255)

                                                                                                     aTCTGCGGCGCCGCCGCCGTGCTGGCATTCTAATCGGCGCTGCGCAGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCAt                                       <  8:117721/147‑1 (MQ=255)

                                                                                                             cggcgccgcggTGCTGGAATTCGCCGCGGCGCGCCCCCCCCCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCATCTGGATAc                               <  1:180816/144‑1 (MQ=255)

                                                                                                                cgccggcgGGCTTGCATTTCAATCGGCGCGGCGCCCCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCATCTGGATACCAt                            <  8:251123/147‑1 (MQ=255)

                                                                                                                  ccgccgTGCTGGCATTCGAATCGGCGCTGCGCCGCGGCCCCCATAAAAGCCCCATGGCACTCGGGAGCGGAGGGCAGTTCGGTACCGTGTCGCAGGTCCGTTACCCCCTGGCCAACAATGCCGGCGGGCTGCATGGGGATTCCATgg                          >  2:50531/1‑147 (MQ=255)

                                                                                                                     ccgTGCTGGCATTCGAATCGGCGCGGCGCAGCCCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCATCTGGATACCATGGgcg                       <  6:216178/147‑1 (MQ=255)

                                                                                                                      cgTGGTGGCTTTCTAATGGGCTGTGCGCTGGGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCATCTGGATACCATGGgcgc                      <  2:178047/147‑1 (MQ=255)

                                                                                                                          cTGGCATTCGAATCGGCGCTGCGCAGCGCCCCCCAAAAAAACGCCAAGGCAGTAGGAAGCGTAGTGCTGTTAGGTAACATGTAGATTTTACATTTACCACTGGCGCTAAATTCCGGCGGGCGGCATATGGATACAAATGGCGCCcgg                  >  8:137046/1‑147 (MQ=255)

                                                                                                                          cTGGCATTCGAATCGGCGCGGCGCAGCGCCCCCCATAAAAGCGGCATGGCAGTCGGGAGCGTAGTGGGGTTGGGTTCCGTGTGGCTGTTGCTTTACCCACTGGCGATAAATGCCGGCTGGCGGGCTCTGGTTTCCATGGGCGCCggg                  >  6:181872/1‑147 (MQ=255)

                                                                                                                          cTGGCATTCGAATCGGCGCGGCCCAGCGCCCCCCATAAAAGCACCATGGCAGTCGGAACCGGAGTGCTGTTCGGTACCGTGTCGCAGTTACATTTCCCACAGTCGAAAAATTCCCCCAGGCAGGATCAGCATAACAAGGGCGccccg                  >  2:227037/1‑144 (MQ=255)

                                                                                                                          cTGCCATTCCACGCGGCGCGGCCCCCCCCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCATCTGGATACCATGGGCGCCggg                  <  5:14317/147‑1 (MQ=255)

                                                                                                                                       cGGCGCTGCGCAGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCATCTGGATACCATGGGCGCCGGGCTGCTGCTGggcg     <  6:255579/147‑1 (MQ=255)

                                                                                                                                          cgcTGCGCAGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCATCTGGATACCATGGGCGCCGGGCTGCTGCTGGGCGGCa  >  5:195897/1‑147 (MQ=255)

TGCTGGTAGTCACCAGTACCCTGCTGATCGGCCTGTGGTGTGGCATGAAAGTGTTCAAGCTCGACCGCGATACCGCCTTGCTGACCGCCGCCGGCAGCGCCATCTGCGGCGCCGCCGCCGTGCTGGCATTCGAATCGGCGCTGCGCAGCGCCCCCCATAAAAGCGCCATGGCAGTCGGAAGCGTAGTGCTGTTCGGTACCTTGTCGATGTTCCTTTACCCACTGGCGATCAATGCCGGCTGGCTGCATCTGGATACCATGGGCGCCGGGCTGCTGCTGGGCGGCA  >  NC_002947_CJ‑RC/4158325‑4158609

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 15 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A