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
A1 F14 I0 R1	248	61.6	2601574	98.7%	2567753	146.9

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	29.7%	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	29.7%	19.5 / 3.3	33	L35R (CTG→CGG)	urtB	urea ABC transporter permease
Reads supporting (aligned to +/- strand): ref base T (11/11); new base G (6/4); total (18/15)
Fisher's exact test for biased strand distribution p-value = 7.12e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GGCTCACCCGCGAAGAATCCAACACCGATTTCCAGGATTGCCCGCATGCTCAGACTCCTGCTCACCCTCCTGCTGCTAATCCCCCTGGCAACCCACGCCAGCGAGGGCGAATTCTTTCTCACCGCCAAGCCCGCCGAGCAGGCCGGCCTGCTCGAAGGCTGGGCAGCACAACCCGATGCCGCGCGCCTGCCGCTGCTGGAAAACCTGCGCCAAGGCCGCATCGCCACCAATGACAAGCGCAAGGTGCGCCTGAACAACCGCCTGCGCGGCCTGATCGACAACGCCCTGGCCA  >  NC_002947_CJ‑RC/5512572‑5512863

ggCCCACCCGCGAAGAATCCAACACCGATTTCCAGGATTGCCCGCATGCTCAGACTCCTGCTCACCCTCCTGCTGCTAATCCCCCTGGCAACCCACGCCAGCGAGGGCGAATTCTTTCTCACCGCCAAGCCCGCCGAGCAGGCCGGCCt                                                                                                                                                 <  3:163500/149‑1 (MQ=255)

 gCTCACCCGCGAAGAATCCAACACCGATTTCCAGGATTGCCCGCATGCTCAGACTCCTGCTCACCCTCCTGCTGCTAATCCCCCTGGCAACCCACGCCAGCGAGGGCGAATTCTTTCTCACCGCCAAGCCCGCCGAGCAGGCCGGCCTg                                                                                                                                                >  6:54679/1‑149 (MQ=255)

         gcgAAGAATCCAACACCGATTTCCAGGATTGCCCGCATGCTCAGACTCCTGCTCACCCTCCTGCTGCTAATCCCCCTGGCAACCCACGCCAGCGAGGGCGAATTCTTTCTCACCGCCAAGCCCGCCGAGCAGGCCGGCCTGCGGGAAgg                                                                                                                                        >  8:293971/1‑149 (MQ=255)

                    aaCACCGATTTCCAGGATTGCCCGCATGCTCAGACTCCTGCTCACCCTCCTGCTGCTAATCCCCCTGGCAACCCACGCCAGCGAGGGCGAATTCTTTCTCACCGCCAAGCCCGCCGAGCGGGCCGGCCGGGGCGAAGGCTggggggcc                                                                                                                              >  1:60842/1‑143 (MQ=255)

                     acacCGATTTCCAGGATTGCCCGCATGCTCAGACTCCTGCTCACCCTCCTGCTGCTAATCCCCCTGGCAACCCACGCCAGCGAGGGCGAATTCTTTCTCACCGCCAAGCCCGCCGAGCAGGCCGGCCTGCTCGAAGGCTGGGCAGcac                                                                                                                             >  7:235640/1‑148 (MQ=255)

                         cGATTTCCAGGATTGCCCGCATGCTCAGACTCCTGCTCACCCTCCTGCTGCTAATCCCCCTGGCAACCCACGCCAGCGAGGGCGAATTCTTTCTCACCGCCAAGCCCGCCGAGCAGGCCGGCCTGCTCGAAGGCTGGGCAGCACAAccc                                                                                                                        >  2:57902/1‑149 (MQ=255)

                                                cTCAGACTCCTGCTCACCCTCCTGCTGCTAATCCCCCTGGCAACCCACGCCAGCGAGGGCGAATTCTTTCTCACCGCCAAGCCCGCCGAGCAGGCCGGGCGGCTCGAAGGCTGGGCAGCACAACCCGATGCCGCGCGCCAGCCcctgct                                                                                                 >  2:252379/1‑149 (MQ=255)

                                                cTCAGACTCCTGCTAACCCTCCTGCTGCTAATCCCCCTGGAAACCCCCTCAAGCTAGGGCGAATTTTTTATCACCGACACGCCCGCCGAGCAGGCGGGCTTGCTCGAAGGCTGGGCAGCACAACCCGATGCCGCGCGCCTGCCgctgct                                                                                                 <  2:39352/149‑1 (MQ=255)

                                                     aCTCCTGCTCACCCTCCTGCTGCTAATCCCCCTGGCAACCCACGCCAGCGAGGGCGAATTCTTTCTCACCGCCAAGCCCGCCGAGCAGGCCGGCCGGCTCGAAGGCTGGGCAGCACAAACCGAATCCGCGCGCCAGCCGCGGCTGGaa                                                                                             >  6:187184/1‑148 (MQ=255)

                                                         ccccccACCCTCCTGCTGCAAATCCCCCAGGCACCCCCCGCCCGCGCGGGCGAATTCTTTCTCACCCCCACCCCCGCCGAGCCGGCCGGCCTGCCCGAAGGCTGGGCAGCACAACCCGATGCCGCGCGCCTGCCGCTGCTGGAAAAc                                                                                          <  5:193877/142‑1 (MQ=255)

                                                            cccACCCTCCTGCTGCAAACCCCCCTGCCACCCCACGCCAGCGAGGGCTAATTCTTTCTCCCCGCCACGCCCGCCGAGCCGGCCGGCCTGCTCGAAGGCTGGGCAGCACAACCCGATGCCGCGCGCCTGCCGCTGCTGGAAAACCTgc                                                                                      <  6:220285/146‑1 (MQ=255)

                                                                 cctcctGCTGCTAATCCCCCTGGCAACCCACGCCAGCGAGGGCGAATTCTTTCTCACCGCCAAGCCCGCCGAGCCCGCCGGCCTGCGCCCAGGCAGGGGAGCACAAACCCCAGCCCCGCCCCGGCCGCAGCTGGAAAACCAGCGCCAAg                                                                                >  6:18209/1‑149 (MQ=255)

                                                                 cctcctGCTGCTAATCCCCCTGGCAACCCACGCCAGCGAGGGCGAATTCTTTCTCACCGCCAAGCCCGCCGAGCAGGCCGGCCTGCTCGAAGGCTGGGCAGCACAACCCCATGCCGCGCGCCTGCCGCTGCTGGAAAACCAGCGCCAAg                                                                                >  2:192085/1‑149 (MQ=255)

                                                                   tcctGCTGCTAATCCCCCTGGCAACCCACGCCAGCGAGGGCGAATTCTTTCTCACCGCCAAGCCCGCCGAGCCGGCCCGGCGGCGCGCACGCTGGGGAGCACAACCCCAAGCCCCCCCCCAGCCCCGGCGGGAAAAACAGCCCCAAAGc                                                                              >  4:75931/1‑149 (MQ=255)

                                                                   tcctGCTGCTAATCCCCCTGGCAACCCACGCCAGCGAGGGCGAATTCTTTCTCACCGCCAAGCCCGCCGAGCAGGCCGGCCTGCTCGAAGGCTGGGCAGCACAACCCCATGCCGCGCGCCGGCCGCGGCTGGAAAACCTGCGCCAAGGc                                                                              >  6:237257/1‑149 (MQ=255)

                                                                             aaTCCCCCTGGCAACCCACGCCAGCGAGGGCGAATTCTTTCTCACCGCCAAGCCCGCCGCGCAGGCCGGCCTGGTCGCAGGCTGGGCAGCACAACCCGATGCCGCGCGCCGGCCGCTGCTGGCAAACCTGCGCCAAGGCCGCCTCGccc                                                                    >  8:296697/1‑148 (MQ=255)

                                                                              aTCCCCCTGGCAACCCACGCCAGCGAGGGCGAATTCTTTCTCACCGCCAAGCCCGCCGAGCACGCCGGCCGGCGCGAAGGCAGGGGAGCCCAAACCCCTGCCCCCCGCCAGCCCCGGCTGGAAAACCAGCGCCCAAGCCGCATAGcccc                                                                   >  4:23822/1‑147 (MQ=255)

                                                                                 ccccTGGCAACCCACGCCAGCGAGGGCGAATTCTTTCTCACCGCCAAGCCCGCCGAGCCGGCCGGCCTGCTCGAAGGCTGGGCAGCCCAACCCGATGCCGCGCGCCTGCCGCTGCGGGAAAACCTGCGCCAAGGCCGCATCGCCACCaa                                                                >  8:70237/1‑149 (MQ=255)

                                                                                    cTGCCACCCCACGCCAGAGCGGGATAATTCTTTCCCCCCCCCCAGCCCGCCGCGCCGGCCGGCCTGCGCGAAGGCTGGGCAGCACAACCCGATGCCGCGCGCCTGCCGCTGCTGGAAAACCTGCGCCAAGGCCGCATCGCCACCAATGa                                                             <  7:293971/149‑1 (MQ=255)

                                                                                       gCAACCCACGCCTGCGTGGGCTATTTCTTTCTCACCGCCACGCCCGCCGTCCAGGCGGGCCGGCTCGAAGGCTGGGCAGCACAACCCGATGCCGCGCGCCTGCCGCTGCTGGAAAACCTGCGCCAAGGCCGCATCGCCACCAATGAc                                                            <  8:130851/147‑1 (MQ=255)

                                                                                         aaCCCACGCCAGCGAGGGCGAATTCTTTCTCACCGCCAAGCCCGCCGCGCCGGCCCGGCGGGGCGCAGGGGGGGCCGCCCCACCCCAAGCCCCGCCCCGGCCGCGGCTGGAAAACCAGCGCCCAGGGCCCCTCGCCACCCAAGACaccc                                                        >  6:41790/1‑146 (MQ=255)

                                                                                                    gCGAGGGCGAATTCTTTCTCACCGCCAAGCCCGCCGAGCAGGCCAGCCTGCTCGAAGGCTGGGCAGCACAACCCGATGCCGCGCGCCTGCCGCTGCTGGAAAACCTGCGCCAAGGCCGCATCGCCACCAATGACAAGCGCAAGGTgcgc                                             <  7:166741/149‑1 (MQ=255)

                                                                                                      gAGGGCTAAATATTCCTCACCGCCCCCCCCGCCCCGCCGGCGGGCCTGCGCGAAGGCTGGGCAGCACAACCCGATGCCGCGCGCCTGCCGCTGCTGGAAAACCTGCGCCAAGGCCGCATCGCCACCAATGACAAGCGCAAGGTGCGCCt                                           <  5:54679/149‑1 (MQ=255)

                                                                                                       agggataaTTATTTCACCCCCCCCCGCCCGCCGCGCCGGCCGGCCTGCGCGAAGGCTGGGCAGCACAACCCGATGCCGCGCGCCTGCCGCTGCTGGAAAACCTGCGCCAAGGCCGCATCGCCACCAATGACAAGCGCAAGGTGCGCCTg                                          <  3:242033/143‑1 (MQ=255)

                                                                                                       aGGGCGAATTCTTTCTCACCGCCAAGCCCGCCGAGCAGGCCGGCCTGCTCGAAGGCTGGGCAGCACAACCCGATGCCGCGCGCCTGCCGCTGCTGGAAAACCTGCGCCAAGGCCGCATCGCCACCAATGACAAGCGCAAGGTGCGCCTg                                          <  8:235640/149‑1 (MQ=255)

                                                                                                         ggCGAATTCTTTCTCACCCCCCCCCCCGCCGCGCAGGCCGGCCGCCCCGAAGGCTGGGCAGCACAACCCGATGCCGCGCGCCTGCCGCTGCTGGAAAACCTGCGCCAAGGCCGCATCGCCACCAATGACAAGCGCAAGGTGCGCCTGaa                                        <  3:114684/149‑1 (MQ=255)

                                                                                                            gAATTCTTTCTCACCGCCAAGCCCGCCGAGCAGGCCGGCCTGCTCGAAGGCTGGGCAGCACCACCCCATGCCGCGCGCCTGCCGCTGCTGGAAAACCTGCGCCAAGGCCGCATCGCCACCAATGACAAGCGCAAGGTGCGCCTGaacaa                                     >  8:76549/1‑149 (MQ=255)

                                                                                                              aTTCTTTCTCACCGCCAAGCCCGCCGAGCCGGCCCGCCAGCTCGAAGGCAGGGCAGCACAACCCCAAGCCGCGCGCCAGCCGCGGCTGGAAAACCAGCCCCCACGCCGCCACGCCCCCAAAGAAAACCCCAAGGAGCGCCAGAACAAcc                                   >  4:281642/1‑149 (MQ=255)

                                                                                                              aTTCTTTCACCCCCCCCCCCCCGCCGCGCCGGCGGCGCGGCGCGAAGGCTGGGCAGCACAACCCGATGCCGCGCGCCTGCCGCTGCTGGAAAACCTGCGCCAAGGCCGCATCGCCACCAATGACAAGCGCAAGGTGCGCCTGAACAAcc                                   <  6:33366/149‑1 (MQ=255)

                                                                                                                        aCCGCCAAGCCCGCCGAGCCGGCCGGCCTGCTCGAAGGCTGGGCAGCACAACACCATCCCGCGCGCCTGCCCCTCCGGGAAAACCACCGCCAAGGCCCCAACGCCACCAATGACAAGCACAAAGTGCGCCAGAACAAACCCCTgcgccg                         >  4:286710/1‑147 (MQ=255)

                                                                                                                          cGCCACGCCCGCCGAGCTGGCCGGCGTGCTCGAAGGCTGGGCAGCACAACCCGATGCCGCGCGCCTGCCGCTGCTGGAAAACCTGCGCCAAGGCCGCATCGCCACCAATGACAAGCGCAAGGTGCGCCTGAACAACCGCCTGCGCGGcc                       <  2:60842/149‑1 (MQ=255)

                                                                                                                             cacgCCCGCCGCGCTGGCCGGCCTGGGCCAAGGCTGGGCAGCACAACCCGATGCCGCGCGCCTGCCGCTGCTGGAAAACCTGCGCCAAGGCCGCATCGCCACCAATGACAAGCGCAAGGTGCGCCTGAACAACCGCCTGCGCGGCCTGa                    <  5:56228/146‑1 (MQ=255)

                                                                                                                             cacccccGCCGAGCCGGCCGGCCGGCGCGAAGGCTGGGCAGCACAACCCGATGCCGCGCGCCTGCCGCTGCTGGAAAACCTGCGCCAAGGCCGCATCGCCACCAATGACAAGCGCAAGGTGCGCCTGAACAACCGCCTGCGCGGCCTGa                    <  1:161967/145‑1 (MQ=255)

                                                                                                                              acgCCCGCCGAGCAGGCCGCCCTGCGCGAAGGCTGGGCAGCACAACCCGATGCCGCGCGCCTGCCGCTGCTGGAAAACCTGCGCCAAGGCCGCATCGCCACCAATGACAAGCGCAAGGTGCGCCTGAACAACCGCCTGCGCGGCCTGAt                   <  5:187184/147‑1 (MQ=255)

                                                                                                                                               cggccggcTCGAAGGCTGGGCAGCACAACCCGATGCCGCGCGCCTGCCGCTGCTGGAAAACCTGCGCCAAGGCCGCATCGCCACCAATGACAAGCGCAAGGTGCGCCTGAACAACCGCCTGCGCGGCCTGATCGACAACGCCCTGgcca  <  3:75931/149‑1 (MQ=255)

                                                                                                                                               cggccggcGCGAAGGCTGGGCAGCACAACCCGATGCCGCGCGCCTGCCGCTGCTGGAAAACCTGCGCCAAGGCCGCATCGCCACCAATGACAAGCGCAAGGTGCGCCTGAACAACCGCCTGCGCGGCCTGATCGACAACGCCCTGgcca  <  5:237257/149‑1 (MQ=255)

GGCTCACCCGCGAAGAATCCAACACCGATTTCCAGGATTGCCCGCATGCTCAGACTCCTGCTCACCCTCCTGCTGCTAATCCCCCTGGCAACCCACGCCAGCGAGGGCGAATTCTTTCTCACCGCCAAGCCCGCCGAGCAGGCCGGCCTGCTCGAAGGCTGGGCAGCACAACCCGATGCCGCGCGCCTGCCGCTGCTGGAAAACCTGCGCCAAGGCCGCATCGCCACCAATGACAAGCGCAAGGTGCGCCTGAACAACCGCCTGCGCGGCCTGATCGACAACGCCCTGGCCA  >  NC_002947_CJ‑RC/5512572‑5512863

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 15 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A