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	5,512,720	T→G	23.8%	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	23.8%	42.4 / 5.7	45	L35R (CTG→CGG)	urtB	urea ABC transporter permease
Reads supporting (aligned to +/- strand): ref base T (14/18); new base G (7/4); total (23/22)
Fisher's exact test for biased strand distribution p-value = 3.10e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCCGCGAAGAATCCAACACCGATTTCCAGGATTGCCCGCATGCTCAGACTCCTGCTCACCCTCCTGCTGCTAATCCCCCTGGCAACCCACGCCAGCGAGGGCGAATTCTTTCTCACCGCCAAGCCCGCCGAGCAGGCCGGCCTGCTCGAAGGCTGGGCAGCACAACCCGATGCCGCGCGCCTGCCGCTGCTGGAAAACCTGCGCCAAGGCCGCATCGCCACCAATGACAAGCGCAAGGTGCGCCTGAACAACCGCCTGCGCGGCCTGATCGACAACGCCCTGG  >  NC_002947_CJ‑RC/5512578‑5512860

cccGCGAAGAATCCAACACCGATTTCCAGGATTGCCCGCATGCTCAGACTCCTGCTCACCCTCCTGCTGCTAATCCCCCTGGCAACCCACGCCAGCGAGGGCGAATTCTTTCTCACCGCCAAGCCCGCCGAGCAGGCCGGCCGGCt                                                                                                                                           >  7:73191/1‑146 (MQ=255)

    ccaagaaTCCAACACCGATTTCCAGGTTTGCCCGCATGCTCAGACTCCTGCTCACCCTCCTGCTGCTAACCCCCCTGGCAACCCACGCCAGCGAGGGCTAATTCTTTCTCACCCCCAAGCCCGCCGAGCAGGCCGGCCTGCTCGAAg                                                                                                                                      <  3:254627/145‑1 (MQ=255)

     gaagaaTCAAACACCGATTTACAGGATTGAACGCATGCTCAGACTCCTGCTCACCCTCCTGCTGCTAAACCACCTGGCAACCCACGCCAGCGAGGGCGAATTATTTCTCACCGCCAAGCCCGCAGAGCACGCCCGCCTTCTCGaacg                                                                                                                                     >  8:238704/1‑145 (MQ=255)

      aagaaTCCAACACCGATTTCCAGGATTGCCCGCATGCTCAGACTCCTGCTCACCCTCCTGCTGCTAATCCCCCTGGCAACCCACGCCAGCGAGGGCGAATTCTTTCTCACCGCCAAGCCCGCCGAGCACCCCCGCCACCTCGaaaa                                                                                                                                     >  3:182052/1‑144 (MQ=255)

            ccAACACCTATTTCCAGGATTGCCCGCATGCTCAGACTCCTGCTCACCCTCCTGCTGCTAATCCCCCTGGCAACCCACGCCAGCGAGGGCGAATTCTTTCTCACCGCCAAGCCCGCCGAGCAGGCCGGCCTGCTCGAAGGCTGGgca                                                                                                                              <  8:1981/147‑1 (MQ=255)

                 acCGATTTCCAGGATTGCCCGCATGCTCAGACTCCTGCTCACCCTCCTGCTGCTAATCCCCCTGGCAACCCACGCCAGCGAGGGCGAATTCTTTCTCACCGCCAAGCCCGCCGAGCCGGCCGGCCGGCGCGAAGGCGGGGCAGcaca                                                                                                                         >  1:224253/1‑147 (MQ=255)

                    gATTTCCAGGATTGCCCGCATGCTCAGACTCCTGCTCACCCTCCTGCTGCTAATCCCCCTGGCAACCCACGCCAGCGAGGGCGAATTCTTTCTCACCGCCAAGCCCGCCGAGCAGGCCGGCCTCCTCGAACGCTGGGGAGCACaaac                                                                                                                      >  5:59741/1‑145 (MQ=255)

                          cAGGATTGCCCGCATGCTCAGACTCCTGCTCACCCTCCTGCTGCTACTCCCCCTGGCAACCCACGCCAGCGAGGGCTAATTCTTTCTCACCGCCAAGCCCGCCGAGCAGGCCGGCCTGCTCGAAGGCTGGGCAGCACAACCCGATGc                                                                                                                <  8:153202/147‑1 (MQ=255)

                              agggCCCGCATGCTCCGACGCCTCCTCCCCCTCCCGCGCATACCCCCCCTCCAACCCCCCGCCCGCGTGGGCTAATTCATACTCCCCCCCACCCCCGCCGCGCCGGCCGGCCTGCTCGAAGGCTGGGCAGCACAACCCGATGCcgcg                                                                                                            <  4:200436/144‑1 (MQ=255)

                                  cccGCATGCTCAGACTCCTGCTCACCCTCCTGCTGCTAATCCCCCTGGCAACCCACGCCAGCGAGGGCGAATTCTTTCTCACCGCCAAGCCCGCCGAGCCGGCCGGCCGGCGCGAAGGCAGGGCAGCACAACCCCATGCCGCGCGcc                                                                                                        >  4:125294/1‑147 (MQ=255)

                                   ccGCATGCTCAGACTCCTGCTCACCCTCCTGCTGCTAATCCCCCTGGCAACCCACGCCAGCGAGGGCGAATTCTTTCTCACCGCCAAGCCCGCCGAGCAGGCCGGCCTGCTCGAAGGCTGGGCAGCACAACCCGATGCCGCGCGCCt                                                                                                       >  2:47913/1‑147 (MQ=255)

                                   ccGCATGCTCAGACTCCTGCTCACCCTCCTGCTGCTAATCCCCCTGGCAACCCACGCCAGCGAGGGCGAATTCTTTCTCACCGCCAAGCCCGCCGAGCAGGCCGGCCGGCGCGAAGGCTGGGCAGCCCAACCCGAAGCcgcccgcca                                                                                                       >  6:10791/1‑146 (MQ=255)

                                       aTGCTCAGACTCCTGCTCACCCTCCTGCTGCTAATCCCCCTGGCAACCCACGCCAGCGAGGGCGAATTCTTTCTCACCGCCAAGCCCGCCGAGCCGGGCGGCCGGGTGGAAGGGTGGGGAGCCCAACCCCATGCCCCGCGCCTGCCg                                                                                                   >  7:262516/1‑147 (MQ=255)

                                           tCAGACTCCTGCTCACCCTCCTGCTGCTAATCCCCCTGGCAACCCACGCCAGCGAGGGCGAATTCTTTCTCACCGCCAAGCCCGCCGAGCAGGCCGGCCAGCTCGAAGGCTGGGCACCCCAACCCCAAGCCGCCCCCCAGCCgcagc                                                                                               >  6:137597/1‑147 (MQ=255)

                                              gACTCCTGCCCACCCTCCTGCTGCAAACCCCCCTGCCACCCCCCCCCAGCGAGGGCTAATTCTTTCTCCCCGCCACGCCCGCCGCGCCGGCCGGCCGGCTCGAAGGCTGGGCAGCACAACCCGATGCCGCGCGCCTGCCgctgct                                                                                              <  7:206983/145‑1 (MQ=255)

                                                cTCCTGCTCACCCTCCTGCTGCTAACCCCCCTGGCAACCCACGCCAGCGAGGGCTAATTCTTTCTCACCGCCACGCCCGCCGAGCAGGCCGGCCTGCTCGAAGGCTGGGCAGCACAACCCGATGCCGCGCGCCTGCCGCTGCTGGaa                                                                                          <  8:198522/147‑1 (MQ=255)

                                                    tGCCCACCCGCCTGCTCCTAACCCCCCTCCCAACCCCCGCCCGCGCGGGCGAATTCTTTCCCCCCGCCCCGCCCGCCGAGCCGGCCGGCCTGCTCGAAGGCTGGGCAGCACAACCCGATGCCGCGCGCCTGCCGCTGCTGGaaaa                                                                                        <  1:91951/145‑1 (MQ=255)

                                                                   tgctAATCCCCCTGGCACCCCCCGCCTGCGTGGGCTAATTGTTTCTCACCGCCACGCCCGCCGAGCCGGCCGGCCTGCTCGAAGGCTGGGCAGCACAACCCGATGCCGCGCGCCTGCCGCTGCTGGAAAACCTGCGCCAAGGCCg                                                                         <  5:66454/145‑1 (MQ=255)

                                                                         tCCCCCTGCCAACCCACCCCAGCGAGGGCTAATTCTACCTCCCCCCCACCCCCGCCCAGCAGGCCGGCCTGCTCGAAGGCTGGGCAGCACAACCCGATGCCGCGCGCCTGCCGCTGCTGGAAAACCTGCGCCAAGGCCGCATCGcca                                                                 <  1:128621/147‑1 (MQ=255)

                                                                             ccaccccacccacccCAGGGGGGGCGATTTCTTTCCCACCCCCACGCCCGCCCCGCCGGGCGGCGGCCGCGAAGGCTGGGCAGCACAACCCGATGCCGCGCGCCTGCCGCTGCTGGAAAACCTGCGCCAAGGCCGCATCGCCACCaa                                                             <  3:118322/140‑1 (MQ=255)

                                                                             ccTGCCAACCCACGCCAGCGTTGGATAATTCTTTCTCACCGCCAAGCCCGCCGAGCTGGCCGGCCTGCTCGAAGGCTGGGCAGCACAACCCGATGCCGCGCGCCTGCCGCTGCTGGAAAACCTGCGCCAAGGCCGCATCGCCACCaa                                                             <  1:237909/147‑1 (MQ=255)

                                                                              cTGCCACCCCCCGCCAGCGAGGGCGAATTCTTTCTAACCGCCTCGCCCGCCGAGCAGGCCGGCCGGCGCGAAGGCTGGGCAGCACAACCCGATGCCGCGCGCCTGCCGCTGCTGGAAAACCTGCGCCAAGGCCGCATCGCCACCAAt                                                            <  8:219669/147‑1 (MQ=255)

                                                                               gggCAACCCCCGCCAGCGTGGGCTATTTCTTTCTCCCCCCCCCGCCCGCCGCGCCGGCCGGCCTGCGCGAAGGCTGGGCAGCACAACCCGATGCCGCGCGCCTGCCGCTGCTGGAAAACCTGCGCCAAGGCCGCATCGCCACCAATg                                                           <  1:150025/146‑1 (MQ=255)

                                                                                  cAACCCACGCCCGCGTGGGCTAATTCTTTCTCACCGCCAAGCCCGCCGAGCAGGCCGGCCTGCTCGAAGGCTGGGCAGCACAACCCGATGCCGCGCGCCTGCCGCTGCTGGAAAACCTGCGCCAAGGCCGCATCGCCACCAATGACa                                                        <  2:224253/147‑1 (MQ=255)

                                                                                  cAACCCACGCCAGCGAGGGCGAATTCTTTCTCACCGCCAAGCCCGCCGAGCAGGCCGGCCGGCTCGAAGGCTGGGCAGCACCACCCCCTGCCGCGCGCCAGCCGCGGCTGGAAAACCAGCGCCAAGGCCGCATCACCACCAATGAc                                                         >  8:1075/1‑146 (MQ=255)

                                                                                           cccgCGAGGGCGAATTCTTTCCCCCCCCCACCCCCGCCGAGCAGGCCGGCCGGCTCGAAGGCTGGGCAGCACAACCCGATGCCGCGCGCCTGCCGCTGCTGGAAAACCTGCGCCAAGGCCGCATCGCCACCAATGACAAGCGCAAgg                                               <  1:59093/144‑1 (MQ=255)

                                                                                           ccAGCGAGGGCGAATTCTTTCTCACCGCCAAGCCCGCCGAGCAGGCCCGCCGGGGCGAAGGGTGGGCCGCCCAACCCCAAGCCGCCCGCCTGGCCCTGCTGGAAAAACAGCGCCAAGGCCCCCTCCCCACCAAAGACAAGCGCAAgg                                               >  6:26522/1‑147 (MQ=255)

                                                                                                   ggttaaTTTTTTCTCACCGCCAAGGCCGCCGTTCTGGGGGGCTTGCTCGAAGGCTGGGCAGCACAACCCGATGCCGCGCGCGTGCCGCTGCTGGAAAACCTGCGCCAAGGCCGCATCGCCACCAATGACAAGCGCAAGGTGCGCCt                                        <  4:182052/142‑1 (MQ=255)

                                                                                                         ttctttctCACCCCCACCCCCGCCGCCCAGGCCGGCCTGCCCGAAGGCTGGGCAGCACAACCCGATGCCGCGCGCCTGCCGCTGCTGGAAAACCTGCGCCAAGGCCGCATCGCCACCAATGACAAGCGCAAGGTGCGCCTGaacaa                                  <  5:10791/146‑1 (MQ=255)

                                                                                                            tttctCACCGCCAAGCCCGCCGAGCAGGCCGGCCTGCTCGAAGGCTGGGCAGCACAACCCGATGCCGCGCGCCTGCCGCTGCTGGAAAACCTGCGCCAAGGCCGCATCGCCACCAATGACAAGCGCAAGGTGCGCCTGAACAACCg                               <  8:73191/146‑1 (MQ=255)

                                                                                                                   ccGCCAAGCCCGCCGAGCAGGCCGGCCTGCTCGAAGGCTGGGCAGCACAACCCGATGCCCCGCGCCTGCCGCTGCTGGAAAACCAGCGCCAAGGCCGCATAGCCACCAATGACAAGCGCAAGGTGCGCCTGAACAACCGCCTGcgcg                       >  8:76199/1‑147 (MQ=255)

                                                                                                                     cccacccccGCCGCGCTGGCCGGCCTGCGCGAAGGCTGGGCAGCACAACCCGATGCCGCGCGCCTGCCGCTGCTGGAAAACCTGCGCCAAGGCCGCATCGCCACCAATGACAAGCGCAAGGTGCGCCTGAACAACCGCCTGCGCGGc                     <  7:222726/141‑1 (MQ=255)

                                                                                                                        aaccccGCCGAGCTGGCCTGACTGCTGGAAGGCTGGGCAGCACAACCCGATGCCTCGCGCCTGCCGCTGCTGGAAAACCTGCGCCAAGGCCGCATCGCCACCAATGACAAGCGCAAGGTGCGCCTGAACAACCGCCTGCGCGGCCTg                  <  3:223924/144‑1 (MQ=255)

                                                                                                                          gCCCGCCGCGCCGGCCGGCCTGCTCGAAGGCTGGGCAGCACAACCCGATGCCGCGCGCCTGCCGCTGCTGGAAAACCTGCGCCAAGGCCGCATCGCCACCAATGACAAGCGCAAGGTGCGCCTGAACAACCGCCTGCGCGGCCTGAt                <  1:196851/147‑1 (MQ=255)

                                                                                                                            ccgccgAGCCGGCCGGCCTGCTCGAAGGCTGGGCAGCACAACCCCCTGCCGCGCGCCGGCCGCTGCTGGAAAAACAGCGCCCACGCCGCATCGCCCCCAATGAAAACCGCCAGGTGAGCCGGAACAACCGCCTGCGCGGCCGGAtag              >  6:171346/1‑145 (MQ=255)

                                                                                                                            ccgccgAGCCGGCCGGCCTGCTCGAAGGCTGGGCAGCACAACCCCAATCCGCGCGCCTGCCGCTGCTGGAAAACCAGCGCCAAGGCCGCCTCGCCAACAAATACAAGCGCAAGGTGCGCCTGAACAACCGCCTGCGCGGCCTGAGCg              >  8:1444/1‑147 (MQ=255)

                                                                                                                            ccgccgAGCAGGCCGGCCTGCTCGAAGGCTGGGCAGCACAACCCCATTCCGCGCGCCTGCCGCTGCTGGAAAACCAGCGCCAAGGCCGCATCGCCACCAATGACAAGCGCAAGGTGCGCCTGAACAACCGCCTGCGCGGCCTGATCg              >  8:5318/1‑147 (MQ=255)

                                                                                                                             cgccgAGCAGGCCGGCCTGCTCGAAGGCTGGGCAGCACCACCCGATGCCGCGCGCCTGCCGCGGCTGGAAAACCAGCGCCAAGGCCGCATCGCCACCAATGACACGCGCAAGGTGCGCCTGAACAACCGCCTGCGCGGCCTGATCg              >  8:153388/1‑146 (MQ=255)

                                                                                                                               tcgAGCAGGCCGGCCTGCTAGAAGGCTGGGCAGCACAACCCGATGCCGCGCGCCTGCCGCTGCTGGAAAACCTGCGCCAAGGCCGCATCGCCCCCAATGACAAGCGCAAGGTGCGCCTGAACAACCGCCTGCGCGGCCTGATCGACa           >  3:42049/2‑147 (MQ=255)

                                                                                                                               ccgAGCAGGCCGGCCTGCTCGAAGGCTGGGCAGCACAACCCGATGCCGCGCGCCTGCCGCTGCTGGAAAACCTGCGCCAAGGCCGCATCGCCACCAATGACAAGCGCAAGGTGCGCCTGAACAACCGCCTGCGCGGCCTGATCGACa           >  5:98221/1‑147 (MQ=255)

                                                                                                                                     aGGCCGGCCTGCTCGAAGGCTGGGCAGCACAACCCGATGCCGCGCGCCTGCCGCTGCTGGAAAACCTGCGCCAAGGCCGCATCGCCACCAATGACAAGCGCAAGGTGCGCCTGAACAACCGCCTGCGCGGCCTGATCGACAACGccc     >  7:245319/1‑147 (MQ=255)

                                                                                                                                        ccggccTGCTCGAAGGCTGGGCAGCACAACCCGATGCCGCGCGCCTGCCGCTGCTGGAAAACCTGCGCCAAGGCCGCATCGCCACCAATGACAAGCGCAAGGTGCGCCTGAACAACCGCCTGCGCGGCCTGATCGACAACGCCCTgg  >  8:158049/1‑147 (MQ=255)

                                                                                                                                        ccggccTGCTCGAAGGCTGGGCAGCACAACCCGATGCCGCGCGCCTGCCGCTGCTGGAAAACCTGCGCCAAGGCCGCATCGCCACCAATGACAAGCGCAAGGTGCGCCTGAACAACCGCCTGCGCGGCCTGATCGACAACGCCCTgg  >  8:185810/1‑147 (MQ=255)

                                                                                                                                        ccggccTGCTCGAAGGCTGGGCAGCACAACCCGATGCCGCGCGCCTGCCGCTGCTGGAAAACCTGCGCCAAGGCCGCATCGCCACCAATGACAAGCGCAAGGTGCGCCTGAACAACCGCCTGCGCGGCCTGATCGACAACGCCCTgg  <  1:271949/147‑1 (MQ=255)

                                                                                                                                          ggccTGCTCGAAGGCTGGGCAGCACAACCCGATGCCGCGCGCCTGCCGCTGCTGGAAAACCTGCGCCAAGGCCGCATCGCCACCAATGACAAGCGCAAGGTGCGCCTGAACACCCGCCTGCGCGGCCTGATCGACAACGCCCTgg  >  7:185505/1‑145 (MQ=255)

CCCGCGAAGAATCCAACACCGATTTCCAGGATTGCCCGCATGCTCAGACTCCTGCTCACCCTCCTGCTGCTAATCCCCCTGGCAACCCACGCCAGCGAGGGCGAATTCTTTCTCACCGCCAAGCCCGCCGAGCAGGCCGGCCTGCTCGAAGGCTGGGCAGCACAACCCGATGCCGCGCGCCTGCCGCTGCTGGAAAACCTGCGCCAAGGCCGCATCGCCACCAATGACAAGCGCAAGGTGCGCCTGAACAACCGCCTGCGCGGCCTGATCGACAACGCCCTGG  >  NC_002947_CJ‑RC/5512578‑5512860

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