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
A3 F14 I0 R1	206	76.7	3255580	98.8%	3216513	146.3

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947_CJ‑RC	5,512,720	T→G	30.4%	L35R (CTG→CGG)	urtB →	urea ABC transporter permease

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947_CJ‑RC	5,512,720	0	T	G	30.4%	58.6 / 7.9	45	L35R (CTG→CGG)	urtB	urea ABC transporter permease
Reads supporting (aligned to +/- strand): ref base T (14/16); new base G (10/3); total (26/19)
Fisher's exact test for biased strand distribution p-value = 9.77e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CTCACCCGCGAAGAATCCAACACCGATTTCCAGGATTGCCCGCATGCTCAGACTCCTGCTCACCCTCCTGCTGCTAATCCCCCTGGCAACCCACGCCAGCGAGGGCGAATTCTTTCTCACCGCCAAGCCCGCCGAGCAGGCCGGCCTGCTCGAAGGCTGGGCAGCACAACCCGATGCCGCGCGCCTGCCGCTGCTGGAAAACCTGCGCCAAGGCCGCATCGCCACCAATGACAAGCGCAAGGTGCGCCTGAACAACCGCCTGCGCGGCCTGATCGACAACGCCCTGGCCAGC  >  NC_002947_CJ‑RC/5512574‑5512865

cTCACCCGCGAAGAATCCAACTGCGATTTCCAGGATTGCCCGCATGCTCAGACTCCTGCTGACCCTCCTGCTGCTAATCCCGCTGGCAACCCACGCCAGCGAGGGCGAATTCTTTCTCACCGCCAAGCCCGCCGAGCAGGCCGGCCTg                                                                                                                                                  <  7:244446/148‑1 (MQ=255)

 tCACCCGCGAAGAATCCAACACCGATTTCCAGGATTGCCCGCATGCTCAGACTCCTGCTCACCCTCCTGCTGCTAATCCCCCTGGCAACCCACGCCAGCGAGGGCGAATTCTTTCTCACCGCCAAGCCCGCCCAGCCGGCCGGCCGGCt                                                                                                                                                >  1:391180/1‑149 (MQ=255)

   aCCCGCGAAGAATCCAACACCGATTTCCAGGATTGCCCGCATGCTCAGACTCCTGCTCACCCTCCTGCTGCTAATCCCCCTGGCAACCCACGCCAGCGAGGGCGAATTCTTTCTCACCGCCAAGCCCGCCGAGCAGGCCGGCCTGCt                                                                                                                                                <  8:56137/147‑1 (MQ=255)

   aCCCGCGAAGAATCCAACACCGATTTCCAGGATTGCCCGCATGCTCAGACTCCTGCTCACCCTCCTGCTGCTAATCCCCCTGGCAACCCACGCCAGCGAGGGCGAATTCTTTCTCACCGCCAAGCCCGCCGAGCAGGCCGGCCTGCt                                                                                                                                                <  8:49832/147‑1 (MQ=255)

     ccGCGAAGAATCCAACACCGATTTCCAGGATTGCCCGCATGCTCAGACTCCTGCTCACCCTCCTGCTGCTAATCCCCCTGGCAACCCACGCCAGCGAGGGCGAATTCTTTCTCACCGCCAAGCCCGCCGAGCAGGCCGGCCTGCTCGa                                                                                                                                             <  5:231796/148‑1 (MQ=255)

      cgcgAAGAATCCAACACCGATTTCCAGGATTGCCCGCATGCTCAGACTCCTGCTCACCCTCCTGCTGCTAATCCCCCTGGCAACCCACGCCAGCGAGGGCGAATTCTTTCTCACCGCCAAGCCCGCCGAGCAGGCCGGCCTGCTCGaa                                                                                                                                            <  8:286700/148‑1 (MQ=255)

        cgAAGAATCCAACACCGATTTCCAGGATTGCCCGCATGCTCAGACTCCTGCTCACCCTCCTGCTGCTAATCCCCCTGGCAACCCACGCCAGCGAGGGCGAATTCTTTCTCACCGCCAAGCCCGCCGAGCAGGCCGGCCTGCGCGAAgg                                                                                                                                          >  7:246412/1‑148 (MQ=255)

           ataaTCCAACACCGATTTCCTGTATTGCCCGCATGCACAGACTCCTGCTCACCCTCCTGCTCCTAATCCCCCTGCCAACCCACGCCCGCGCGGGCTAATTCTTTCTCCCCCCCAACCCCGCCGAGCTGGCCGGCCTGCTCGAAGGCt                                                                                                                                        <  4:90923/145‑1 (MQ=255)

           agaaTCCAACACCGATTTCCAGGATTGCCCGCATGCTCAGACTCCTGCTCACCCTCCTGCTGCTAATCCCCCTGGCAACCCACGCCAGCGAGGGCGAATTCTTTCTCACCGCCAAGCCCGCCGAGCAGGCCGGCCTGCTCGAAGGCt                                                                                                                                        <  2:65517/147‑1 (MQ=255)

                ccAACACCGATTTCCAGGATTGCCCGCATGCTCAGACTCCTGCTCACCCTCCTGCTGCTAATCCCCCTGGCAACCCACGCCAGCGAGGGCGAATTCTTTCTCACCGCCAAGCCCGCCGAGCAGGCCGGCCGGCTCGAAGGCGGGgcag                                                                                                                                  >  8:353370/1‑148 (MQ=255)

                 cAACACCCATTTCCCGCATTGCCCGCATCCTCCGACTCCTGCTCACCCTCCTGCTGCTAACCCCCCTGGCAACCCACGCCCGCGAGGGCGAATTCTTTCTCACCGCCAAGCCCGCCGCGCAGGCCGGCCTGCTCGAAGGCTGGgcagca                                                                                                                                <  2:360115/149‑1 (MQ=255)

                     acCTATTTCCTGTATTGCCCGCATGCTCACACTCCGCCTCACCCTCCTGCTGCAAAACCCCCTGCCAACCCACCCCAGCGTGGGCTAATTCTTTCACACCGCCAACCCCGCCGAGCCGGCCGGCCTGCTCGAAGGCTGGGCAGCACAAc                                                                                                                            <  4:60557/149‑1 (MQ=255)

                     acCGATTTCCAGGATTGCCCGCATGCTCAGACTCCTGCTCACCCTCCTGCTGCTAATCCCCCTGGCAACCCACGCCAGCGAGGGCGAATTCTTTCTCACCGCCAAGCCCGCCGAGCAGGCCGGCCTGCGCGAAGGCTGGGCAGCACAAc                                                                                                                            >  1:52472/1‑149 (MQ=255)

                                      cccGCATGATCAGACTACTGCTCAACCTCCTCCTGCTAATCCCCCTGGCAACCAACGCCAGCGAGGGCGAATTCTTTCTCCCCGCCAACCCCGCCCCCCAGGCCCGCCTGGAACAAGGGAGGGCAGACCCACCCCATGCCCCGCGccag                                                                                                           >  2:104359/1‑147 (MQ=255)

                                                     tCCTGCTCACCCTCCTGCTGCTAATCCCCCTGGCAACCCACGCCAGCGAGGGCGAATTCTTTCTCACCGCCAAGCCCGCCGAGCCGGCCGGCCGGCTCGAAGGCTGGGGAGCACAACCCCAAGCCGCCCGCCGGCCCCGGCTGGaaaa                                                                                             >  1:103883/1‑148 (MQ=255)

                                                          cccacccaccTGCTCAAAACCCCCCTCCCACCCCCCGCCGGCGGGGTCTATTTTTTTCACCCCCCAACCCCCGCCGAGCTGGCGGGCCGGCTCGAAGACTGGGCAGCACAACCCGATGCCGCGCGCCTGCCGCTGCTGGAAAACCTgc                                                                                        <  4:39375/146‑1 (MQ=255)

                                                          cccACCCTCCTGCTCCAAACCCCCCCGGCACCCCCCGCCCGCGCGGGCGAATTCTTTCCCCCCCCCCCCCCCGCCGCGCCGGCCGGCCGGCGCGAAGGCTGGGCAGCACAACCCGATGCCGCGCGCCTGCCGCTGCTGGAAAACCTg                                                                                         <  1:261468/145‑1 (MQ=255)

                                                          cTCACCCTCCTGCTGCTAATCCCCCTGGCAACCCACGCCAGCGAGGGCTAATTCTTTCTCACCGCCAAGCCCGCCGAGCAGGCCGGCCTGCTCGAAGGCTGGGCAGCACAACCCGATGCCGCGCGCCTGCCGCTGCTGGAAAACCTgc                                                                                        <  8:196838/148‑1 (MQ=255)

                                                           tCACCCTCCTGCTGCTAATCCCCCTGGCAACCCACGCCAGCGAGGGCGAATTCTTTCTCACCGCCAAGCCCGCCGAGCAGGCCGGCCGGCGCCAACGCTGGGCAGCCCAACCCCCAGCCCCGCGCCTGCCGCAGCTGGAAAACCAgcgc                                                                                      >  1:26846/1‑149 (MQ=255)

                                                             aCCCTCCTGCTGCTAATCCCCCTGGCAACCCACGCCAGCGAGGGCGAATTCTTTCTCACCGCCAAGCCCGCCGAGCCGGCCGGCCGGGGCGCAGGCGGGGGCGCCCCACCCCCAGCCCCGCCCCCGCCGCGGCGGGAAAACCAGCGcc                                                                                     >  1:166360/1‑148 (MQ=255)

                                                             aCCCTCCTGCTGCTAATCCCCCTGGCAACCCACGCCAGCGAGGGCGAATTCTTTCTCACCGCCAAGCCCGCCGAGCCGGCCCGCCGGCGCGAAGGCTGGGCAGCACAACCCCAAGCCCCGCGCCAGCCGCGGCTGGAAAACCACCGcc                                                                                     >  4:371043/1‑148 (MQ=255)

                                                             aCCCTCCTGCTGCTAATCCCCCTGGCAACCCACGCCAGCGAGGGCGAATTCTTTCTCACCGCCAAGCCCGCCGAGCACGCCCGCCGGCACGAAGGCTGGGCCGCCCAACCCGAATCCCCGCGCCTGCCCCGGCTGGAAAACCATCGcc                                                                                     >  2:8678/1‑148 (MQ=255)

                                                              cccTCCTGCTGCTAATCCCCCTGGCAACCCACGCCAGCGAGGGCGAATTCTTTCTCACCGCCAAGCCCGCCGAGCAGGCCCGCCGGCGCGCAGGCTGGGGCGCACCACCCCCTGCCCCCCGCCTGCCGCGGCTGGGAAACCAGCGcc                                                                                     >  5:339398/1‑147 (MQ=255)

                                                                  cctGCTGCTAATCCCCCTGGCAACCCACGCCAGCGAGGGCGAATTCTTTCTCACCGCCAAGCCCGCCGAGCAGGCCGGCCCGGGCGAAGGCTGGGGAGCCCCACCCCCAGCCGCCCGCCAGCCGCGGCGGGCAAAACAGCGCCAAGGcc                                                                               >  2:143633/1‑149 (MQ=255)

                                                                       tgctAATCCCCCTGGCAACCCACGCCAGCGAGGGCGAATTCTTTCTCACCGCCAAGCCCGCCGAGCCGGCCGGCCTGCGCGAAGGCTGGGCCGCACAACCCCAAGCCGCGCGCCTGCCGCTGCTGGAAAACCAGCGCCAAGGCCGCATc                                                                          >  3:210324/1‑149 (MQ=255)

                                                                            aTCCCCCTGGCAACCCACGCCAGCGAGGGCGAATTCTTTCTCACCGCCAAGCCCGCCGAGCAGGCCGGCCTGCTCGAAGGCTGGGCAGCACAACCCGATGCCGCGCGCCTGCCGCTGCTGGAAAACCTGCGCCAAGGCCGCATCGcca                                                                      <  2:52472/148‑1 (MQ=255)

                                                                               ccccTGCCAACCCACGCCAGCGAGGGAGAATTCTTTCTCACCGCCAACCCCGCCGAGCAGGCCGGCCTGCTCGAAGGCTGGGCAGCACAACCCGATGCCGCGCGCCTGCCGCTGCTGGAAAACCTGCGCCAAGGCCGCATCGccacca                                                                   <  8:246412/148‑1 (MQ=255)

                                                                                       acccccCGCCAGCGTTGGCTAATTCTTTCTCCCCGCCACGCCCGCCGCGCCGGCCGGCCTGCTCGAAGGCTGGGCAGCACAACCCGATGCCGCGCGCCTGCCGCTGCTGGAAAACCTGCGCCAAGGCCGCATCGCCACCAATGACAAg                                                           <  5:239113/146‑1 (MQ=255)

                                                                                          ccACGCCAGCGAGGGCGAATTCTTTCTCACCGCCAAGCCCGCCGAGCAGGCCGGCCTGCTCGAAGGCTGGGCAGCACAACCCGATGCCGCGCGCCTGCCGCAGCTGGAAAACCAGCGCCAAGGCCGCCTCGCCCCCAATGACAAgcgc                                                        >  2:101430/1‑148 (MQ=255)

                                                                                           cccGCCAGCGTGGGAGAATTCTTTCTCCCCCCCAACCCCGCCGAGCAGCCGGGCCTGCTCGAAGGCTGGGCAGCACAACCCGATGCCGCGCGCCTGCCGCTGCTGGAAAACCTGCGCCAAGGCCGCATCGCCACCAATGACAAGCGCa                                                       <  7:311196/146‑1 (MQ=255)

                                                                                                        gCGAATTCTTTCTCACCGCCAAGCCCGCCGAGCAGGCCGGCCTGCTCGAAGGCTGGGCAGCACAACCCCAAGCCCCGCGCCTGCCGCTGCTGGAAAACCAGCGCCAAGGCCGCATCGCCACCAAAGACAAGCGCAAGGTGAGCCGGaa                                          >  2:209102/1‑148 (MQ=255)

                                                                                                            attattTCTCCCCCCCACGCCCGCCGAGCTGGCGGGCCTGCGCGAAGGCTGGGCAGCACAACCCGATGCCGCGCGCCTGCCGCTGCTGGAAAACCTGCGCCAAGGCCGCATCGCCACCAATGACAAGCGCAAGGTGCGCCTGaacaac                                      <  2:103883/148‑1 (MQ=255)

                                                                                                                 ttctCACCGCCAAGCCCGCCGAGCAGGCCGGCCGGCTCGAAGGCTGGGCAGCACAACCCCATGCCCCGCGCCAGCCGCTGCTGGAAAAACAGCGCCAAGGCCCCATCGCCCCCAATGACAAACGCAAGGTGCGCCTGAACAAcccc                                   >  8:139306/1‑144 (MQ=255)

                                                                                                                  tctcACCGCCAAGCCCGCCGAGCAGGCCGGCCAGCTCGAAGGCTGGGCCGCACAACCCCAATCCGCGCCCCAGCCGCTGCTGGAAAACCAGCGCCAAAGCCCCATCGCCCCCAAATACAACCGCAAGGTGCGCCTGAACAACCCCCTgc                               >  2:209507/1‑149 (MQ=255)

                                                                                                                     cACCGCCAAGCCCGCCGAGCCCGCCGGCCGGCTCGCAAGCTGGGCAGCACAAACCCAAGCCCCCCCCCAGCCCCAGCGGGTAAACCAGCGCCCAAGCCGCAAAGCCCCCAAAGAAAAACCCAAAGTGCGCCTGAACAACccccgacgc                             >  6:252087/1‑143 (MQ=255)

                                                                                                                       cccccACGCCCGCCGAGCCGGCCGGCCGGCTCGAAGGCTGGGCAGCACAACCCGATGCCGCGCGCCTGCCGCTGCTGGAAAACCTGCGCCAAGGCCGCATCGCCACCAATGACAAGCGCAAGGTGCGCCTGAACAACCGCCTGCGCgg                           <  5:252087/145‑1 (MQ=255)

                                                                                                                       ccGCCAAGCCCGCCGAGCAGGCCGGCCTGCTCGAAGGCTGGGCAGCACAACCCGATGCCGCGCGCCTGCCGCTGCTGGAAAACCTGCGCCAAGGCCGCATCGCCACCAATGACAAGCGCAAGGTGCGCCTGAACAACCGCCTGCGCgg                           >  6:163240/1‑148 (MQ=255)

                                                                                                                               cccGCCGAGCAGGCCGGCCTGCTCGAAGGCTGGGCAGCACAACCCGCTGCCGCGCCCCTGCCGCTGCTGGAAAACCAGCGCCAAGGCCGCCTCGCCACCAATGACAAGCGCAAGGTGCGCCTGAACAACCGCCAGCGCGGCCTGa                      >  8:139949/1‑145 (MQ=255)

                                                                                                                                cccccgAGCCGGCGGGCCTGCTCGAAGGCTGGGCAGCACAACCCGATGCCGCGCGCCTGCCGCTGCTGGAAAACCTGCGCCAAGGCCGCATCGCCACCAATGACAAGCGCAAGGTGCGCCTGAACAACCGCCTGCGCGGCCTGATCGAc                 <  2:340708/146‑1 (MQ=255)

                                                                                                                                   tcgAGCAGGCCGGCCTGCTAGAAGGCTGGGCAGCACAACCCGATGCCGCGCGCCTGCCGCTGCTGGAAAACCTGCGCCAAGGCCGCATCGCCACCAATGACAAGCGCAAGGTGCGCCTGAACACCCGCCTGCGCGGCCTGATCGACaa               >  6:197264/2‑148 (MQ=255)

                                                                                                                                       gCAGGCCGGCCTGCTCGAAGGCTGGGCAGCACAACCCGATGCCGCGCGCCTGCCGCTGCTGGAAAACCTGCGCCAAGGCCGCATCGCCACCAATGACAAGCGCAAGGTGCGCCTGAACAACCGCCTGCGCGGCCTGATCGACAACGccc          >  4:345595/1‑149 (MQ=255)

                                                                                                                                          ggccggccTGCTCGAAGGCTGGGCAGCACAACCCGATGCCGCGCGCCTGCCGCTGCTGGAAAACCTGCGCCAAGGCCGCATCGCCACCAATGACAAGCGCAAGGTGCGCCTGAACAACCGCCTGCGCGGCCTGATCGACAACGCCCTgg       >  3:388298/1‑149 (MQ=255)

                                                                                                                                          ggccggccTGCTCGAAGGCTGGGCAGCACAACCCGATGCCGCGCGCCTGCCGCTGCTGGAAAACCTGCGCCAAGGCCGCATCGCCACCAATGACAAGCGCAAGGTGCGCCTGAACAACCGCCTGCGCGGCCTGATCGACAACGCCCTgg       >  3:294391/1‑149 (MQ=255)

                                                                                                                                           gccggccTGCTCGAAGGCTGGGCAGCACAACCCGATGCCGCGCGCCTGCCGCTGCTGGAAAACCTGCGCCAAGGCCGCATCGCCACCAATGACAAGCGCAAGGTGCGCCTGAACAACCGCCTGCGCGGCCTGATCGACAACGCCCTgg       >  5:129979/1‑148 (MQ=255)

                                                                                                                                               accTGCTCGAAGGCTGGGCAGCACAACCCGATGCCGCGCGCCTGCCGCTGCTGGAAAACCTGCGCCAAGGCCGCATCGCCACCAATGACAAGCGCAAGGTGCGCCTGAACAACCGCCTGCGCGGCCTGATCGACAACGCCCTGgccagc  >  3:109320/2‑149 (MQ=255)

CTCACCCGCGAAGAATCCAACACCGATTTCCAGGATTGCCCGCATGCTCAGACTCCTGCTCACCCTCCTGCTGCTAATCCCCCTGGCAACCCACGCCAGCGAGGGCGAATTCTTTCTCACCGCCAAGCCCGCCGAGCAGGCCGGCCTGCTCGAAGGCTGGGCAGCACAACCCGATGCCGCGCGCCTGCCGCTGCTGGAAAACCTGCGCCAAGGCCGCATCGCCACCAATGACAAGCGCAAGGTGCGCCTGAACAACCGCCTGCGCGGCCTGATCGACAACGCCCTGGCCAGC  >  NC_002947_CJ‑RC/5512574‑5512865

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