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	4,442,726	A→C	26.9%	intergenic (‑89/+49)	nicP‑II ← / ← nicT	porin‑like protein/metabolite transport protein NicT

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947_CJ‑RC	4,442,726	0	A	C	26.9%	34.9 / 5.2	36	intergenic (‑89/+49)	nicP‑II/nicT	porin‑like protein/metabolite transport protein NicT
Reads supporting (aligned to +/- strand): ref base A (9/15); new base C (8/2); total (17/19)
Fisher's exact test for biased strand distribution p-value = 5.70e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CAACCGCCGGCCAGGCGTGCAGACGAAGAAAAACGCGGCGCAGTGAAACCTTGCATAGGGCTACTCCTGGATTTGGGCAACAGCAACCCGGCGCGGCGGCACTGCATGGCCACCGGCGTGCGGGTTGCATCGAGAGAGGTCGGCAGGCGGGCCCCGGCCCGCCTGCCCTGCCGTTGCGTGAAGCGCTGGGCCGCTAGCGGTTGACCAGCTTGGCCGGCAAGGCGATGACCAGGAAGCAGCTGAGGATCAGGCAGCCGGCAAACACCCACAGCGCAGCGTGCGAGGTGCCGG  >  NC_002947_CJ‑RC/4442582‑4442872

cAACCGCCGGCCAGGCGTGCAGACGAAGAAAAACGCGGCGCAGTGAAACCTTGCATAGGGCTACTCCTGGATTTGGGCAACAGCAACCCGGCGCGGCGGCACTGCATGGCCACCGGCGTGCGGGTTGCATCGAGAGAGGTCGGCAgg                                                                                                                                                  >  2:38778/1‑147 (MQ=255)

   ccgccgGCCAGGCGTGCAGACGAAGAAAAACGCGGCGCAGTGAAACCTTGCATAGGGCTACTCCTGGATTTGGGCAACAGCAACCCGGCGCGGCGGCACTGCATGGCCACCGGCGTGCGGGTTGCATCGAGAGAGGTCGGCACGCgg                                                                                                                                               >  2:94047/1‑147 (MQ=255)

      ccgGCCAGGCGTGCAGACGAAGAAAAACGCGGCGCAGTGAAACCTTGCATAGGGCTACTCCTGGATTTGGGCAACAGCAACCCGGCGCGGCGGCACTGCATGGCCACCGGCGTGCGGGTTGCATCGAGAGAGGTCGGCAGGCGGGcc                                                                                                                                            <  7:151828/147‑1 (MQ=255)

        ggCCAGGCGTGCAGACGAAGAAAAACGCGGCGCAGTGAAACCTTGCATAGGGCTACTCCTGGATTTGGGCAACAGCAACCCGGCGCGGCGGCACTGCATGGCCACCGGCGTGCGGGTTGCATCGAGAGAGGTCCGGAGGGGGGcccc                                                                                                                                          >  3:264036/1‑147 (MQ=255)

               cGTGCAGACGAAGAAAAACGCGGCGCAGTGAAACCTTGCATAGGGCTACTCCTGGATTTGGGCAACAGCAACCCGGCGCGGCGGCACTGCATGGCCACCGGCGTGCGGGTTGCATCGAGAGAGGTCGGCCGGCGGGCCCCCGcccc                                                                                                                                    >  2:119921/1‑145 (MQ=255)

               cGTGCAGACGAAGAAAAACGCGGCGCAGTGAAACCTTGCATAGGGCTACTCCTGGATTTGGGCAACAGCAACCCGGCGCGGCGGCACTGCATGGCCACCGGCGTGCGGGTTGCATCGAGAGAGGTCGGCCCGCGGGCCCCGGCCCg                                                                                                                                    >  5:147651/1‑146 (MQ=255)

                     gACGAAGAAAAACGCGGCGCAGTGAAACCTTGCATAGGGCTACTCCTGGATTTGGGCAACAGCAACCCGGCGCGGCGGCACTGCATGGCCACCGGCGTGCGGGTTGCATCGAGAGAGGTCGGCAGGCGGGCCCCCGCCCCccagc                                                                                                                               >  8:89701/1‑145 (MQ=255)

                       cGAAGAAAAACGCGGCGCAGTGAAACCTTGCATAGGGCTACTCCTGGATTTGGGCAACAGCAACCCGGCGCGGCGGCACTGCATGGCCACCGGCGTGCGGGTTGCATCGAGAGAGGTCGGCCGGCGGGCCCCGGCCCCccagcccag                                                                                                                           >  1:178273/1‑145 (MQ=255)

                           gaaAAACGCGGCGCAGTGAAACCTTGCATAGGGCTACTCCTGGATTTGGGCAACAGCAACCCGGCGGGGGGGCACTGCATGGCCACCGGGGTGGGGGTTGAATCGAGAGAGGTCGGCAGGCGGGCCCCGGCCCGCCTGCCCTGCCGt                                                                                                                       <  6:237828/147‑1 (MQ=255)

                            aaaaaCGCGGCGCAGTGAAACCTTGCATAGGGCTACTCCTGGATTTGGGCAACAGCAACCCGGCGCGGCGGCACTGCATGGCCACCGGCGTGCGGGTTGCATCGAGAGAGGTCGGCCGGCGGGCCCCGGCCCGCCTGCCCTGCCggt                                                                                                                      >  8:34770/1‑145 (MQ=255)

                                                          ggCTACTCCTGGATTTGGGCAACAGCAACCCGGCGCGGCGGCACTGCATGGCCACCGGCGTGCGGGTTGCATCGAGAGAGGTCGGCAGGCGGGCCCCGGCCCGCCTGCCCTGCCGTTGCGTGAAGCGCTGGGCCGCTAGCGGTTGa                                                                                         <  6:187314/146‑1 (MQ=255)

                                                                   tGGATTTGGGCAACAGCAACCCGGCGCGGCGGCACTGCATGGCCACCGGCGTGCGGGTTGCATCGAGAGAGGTCGGCCGGCGGGCCCCCGCCCCCCTGCCCTGCCGTTGGGTGAAGCGCGGGGCCGCGAGCGGTTGGCCAGcgttgc                                                                               >  1:7849/1‑142 (MQ=255)

                                                                           ggCAACAGCAACCCGGCGCGGCGGCACTGCATGGCCACCGGCGTGCGGGTTGCATCGAGAGAGGTCGGCCGGCGGGCCCCCGCCCGCCAGCCCAGGCCTTGCGTGAAGCCCAGGGCCGCTAGCGGGTGACCACCTTTGCCGGCAAgg                                                                       >  8:119280/1‑147 (MQ=255)

                                                                           ggCAACAGCAACCCGGCGCGGCGGCACTGCATGGCCACCGGCGTGCGGGTTGCATCGAGAGAGGTCGGCAGGCGGGCCCCGGCCCGCCTGCCCTGCCGTTGCGTGAAGCGCTGGGCCGCTAGCGGTTGACCAGCTTGGCCGGCAAg                                                                        <  8:140669/146‑1 (MQ=255)

                                                                           ggCAACAGCAACCCGGCGCGGCGGCACTGCATGGCCACCGGCGTGCGGGTTGCATCGAGAGAGGTCGGCAGGCGGGCCCCCGCCCCCCAGCCCGGCCCTTTCGGGAAGCGCGGGGGCGCGAGCGGGTGACCAGCGTTGGCGGGAAgg                                                                       >  2:93659/1‑147 (MQ=255)

                                                                             cAACAGCAACCCGGCGCGGCGGCACTGCATGGCCACCGGCGTGCGGGTTGCATCGAGAGAGGTCGGCAGGCGGGCCCCGGCCCGCCAGCCCGGGCGTTGCGTGTAGCGCTGGGCCGCGAGCGGGTGGCCAGCTTGGCCGGCCAGGCg                                                                     >  6:238131/1‑147 (MQ=255)

                                                                                 aGCAACCCGGCGCGGCGGCACTGCATGGCCACCGGCGTGCGGGTTGCATCGAGAGAGGTCGGCAGGCGGGCCCCGGCCCGCCTGCCCTGCCGTTGCGTGAAGCGCTGGGCCGCTAGCGGTTGACCAGCTTGGCCGGCAAGGCGATGa                                                                 <  6:243290/147‑1 (MQ=255)

                                                                                 aGCAACCCGGCGCGGCGGCACTGCATGGCCACCGGCGTGCGGGTTGCATCGAGAGAGGTCGGCAGGCGGGCCCCGGCCCGCCTGCCCTGCCGTTGCGTGAAGCGCTGGGCCGCTAGCGGTTGACCAGCTTGGCCGGCAAGGCGATGa                                                                 <  8:14992/147‑1 (MQ=255)

                                                                                  gCAACCCGGCGCGGCGGCACTGCATGGCCACCGGCGTGCGGGTTGCATCGAGAGAGGTCGGCAGGCGGGCCCCGGCCCGCCTGCCCTGCCGTTGCGTGAAGCGCTGGGCCGCTAGCGGTTGACCAGCTTGGCCGGCAAGGCGATGAc                                                                <  6:181766/147‑1 (MQ=255)

                                                                                   cAACCCGGCGCGGCGGCACTGCATGGCCACCGGCGTGCGGGTTGCATCGAGAGAGGTCGGCAGGCGGGCCCCGGCCCGCCAGCCCAGCCGTTTCGTGAAGCGCTGGGCCGCTAACCGTTGACCAACTTGGCCCGCAAGGCCATAAc                                                                >  4:183730/1‑146 (MQ=255)

                                                                                    aaCCGGGCGGGGGGGCACTGCAGGGCCACGGGGGTGCGGGTTGCATCGAGCGAGGGCGGCAGGCGGGCCCCGGCCCGCCTGCCCTGCCGTTGCGTGAAGCGCTGGGCCGCTAGCGGTTGACCAGCTTGGCCGGCAAGGCGATGACCa                                                              <  8:103003/147‑1 (MQ=255)

                                                                                     aCCCGGCGCGGCGGCACTGCATGGCCACCGGCGTGAGGGTTGCATCGAGAGAGGTCGGCAGGCGGGCCCCGGCCCGCCTGCCCTGCCGTTGCGTGAAGCGCTGGGCCGCTAGAGGTTGGCCAGCTTGGCCGGCAAGGCGATGACCAg                                                             >  2:158866/1‑147 (MQ=255)

                                                                                       ccGGCGCGGCGGCACTGCATGGCCACCGGCGTGCGGGTTGCATCGAGAGAGGTCGGCAGGCGGGCCCCGGCCCGCCTGCCCTGCCGTTTCGTGAAGCGCTGGGCCGCTAGCGGTTGACCAGCTTGGCCGGCAAGGCGATGACCAg                                                             >  6:133479/1‑145 (MQ=255)

                                                                                                cggcACTGCATGGCCACCGGCGTGGGGGTTGCATGTAGTGTGGTCGGCAGGCGGGCCCCGGCCCGCCTGCCCTGCCGTTGCGTGAAGCGCTGGGCCGCTAGCGGTTGACCAGCTTGGCCGGCAAGGCGATGACCAGGAAGCAGCTGa                                                  <  8:51936/147‑1 (MQ=255)

                                                                                                 ggcACTGCATGGCCACCGGCGTGCGGGTTGCATCGAGAGAGGTCGGCCGGCGGGCCCCCGCCCCCCGGCCCGGCCGTTGGGGGGAGCGCGGGGGCGCTAGCGGTTGCCCCGCGTTGCCGGCAAGGCGCTGGCCAGGGAGCAGCGGAg                                                 >  6:52880/1‑147 (MQ=255)

                                                                                                    aCTGCATGGCCCCCGGCGGGCGGGTTGCTTCGAGATAGGTCGGCTGGCGGGCCCCGGCCCGCCTGCCCTGCCGTTGCGTGAAGCGCTGGGCCGCTAGCGGTTGACCAGCTTGGCCGGCAAGGCGATGACCAGGAAGCAGCTGAGGAt                                              <  1:60042/147‑1 (MQ=255)

                                                                                                     cTGCAGGCCCACCGGCGTGCGGGTTGCATCGAGAGAGGGCGGCAGGGGGGCCCCGGCCCGCCTGCCCTGCCGTTGCGTGAAGCGCTGGGCCGCTAGCGGTTGACCAGCTTGGCCGGCAAGGCGATGACCAGGAAGCAGCTGAGGATc                                             <  7:63649/147‑1 (MQ=255)

                                                                                                         aTGGCCACCGGCGTGCGGGTTGCATCGAGAGAGGTCGGCCGGCGGGCCCCCGCCCGCCTGCCCAGCCGTTGGGTGAAGCGCTGGGCCGCTATCGGTTGACCAGCTTTGCCGGCAAGGCGATGACCACGAAGCAGCTGACGCTCac                                           >  6:260155/1‑144 (MQ=255)

                                                                                                              cACCGGCGTGCGGGTTGCATCGAGAGAGGTCGGCAGGCGGGCCCCGGCCCGCCTGCCCTGCCGTTGCGTGAAGCGCTGGGCCGCTAGCGGTTGACCAGCTTGGCCGGCAAGGCGATGACCAGGAAGCAGCTGAGGATCAGGCAGCCg                                    <  8:68192/147‑1 (MQ=255)

                                                                                                                cgggggTGGGGGTTGCTTCTTGTGTGGGCGGCTGGCGGGCCCGGCCCCGCCTGCCCTGCCGTTGCGTGAAGCGCTGGGCCGCTAGCGGTTGACCAGCTTGGCCGGCAAGGCGATGACCAGGAAGCAGCTGAGGATCAGGCAGCCGGc                                  <  4:189762/142‑1 (MQ=255)

                                                                                                                ccGGCGTGCGGGTTGCATCGTGAGAGGTCGGCAGGCGGGCCCCGGCCCGCCTGCCCTGCCGTTGCGTGAAGCGCTGGGCCGCTAGCGGTTGACCAGCTTGGCCGGCAAGGCGATGACCAGGAAGCAGCTGAGGATCAGGCAGCCGGc                                  <  6:195484/147‑1 (MQ=255)

                                                                                                                     gTGCGGGTTGCATCGATTTTGGTCGGCAGGCGGGCCCCGGCCCGCCTGCCCTGCCGTTGCGTGAAGCGCTGGGCCGCTAGCGGTTGACCAGCTTGGCCGGCAAGGCGATGACCAGGAAGCAGCTGAGGATCAGGCAGCCGGCAAaca                             <  6:199215/147‑1 (MQ=255)

                                                                                                                                 tCGCGAGCGGCCGGCCGGCGGCCCCCGGCCCGCCTGCCCTGCCGTTGCGTGAAGCGCTGGGCCGCTAGCGGTTGACCAGCTTGGCCGGCAAGGCGATGACCAGGAAGCAGCTGAGGATCAGGCAGCCGGCAAACACCCAcagcgcag                 <  1:119921/147‑1 (MQ=255)

                                                                                                                                    agatcggTCGGCCGGCGGGCCCCGGCCCGCCTGCCCTGCCGTTGCGTGAAGCGCTGGGCCTCTAGCGGTTGACCAGCTTGGCCTTCAAGGCGATGACCAGGAAGCAGCTGAGGATCAGGCAGCCGGCAAACACCCAcagcgcagcg               <  7:38330/141‑1 (MQ=255)

                                                                                                                                              gCAGGCGGGCCCCGGCCCGCCTGCCCTGCCGTTGCGTGAAGCGCTGGGCCGCTAGCGGTTGACCAGCTTGGCCGGCAAGGCGATGACCAGGAAGCAGCTGAGGATCAGGCAGCCGGCAAACACCCACAGCGCAGCGTGCGAGGTGcc    <  4:34511/147‑1 (MQ=255)

                                                                                                                                               cAGGCGGGCCCCGGCCCGCCTGCCCTGCCGTTGCGTGAAGCGCTGGGCCGCTAGCGGTTGACCAGCTTGGCCGGCAAGGCGATGACCAGGAAGCAGCTGAGGATCAGGCAGCCGGCAAACACCCACAGCGCAGCGTGCGAGGTGCCg   <  6:124329/147‑1 (MQ=255)

                                                                                                                                                aGGCGGGCCCCGGCCCGCCTGCCCTGCCGTTGCGTGAAGCGCTGGGCCGCTAGCGGTTGACCAGCTTGGCCGGCAAGGCGATGACCAGGAAGCAGCTGAGGATCAGGCAGCCGGCAAACACCCACAGCGCAGCGTGCGAGGTGCCgg  >  1:119244/1‑147 (MQ=255)

CAACCGCCGGCCAGGCGTGCAGACGAAGAAAAACGCGGCGCAGTGAAACCTTGCATAGGGCTACTCCTGGATTTGGGCAACAGCAACCCGGCGCGGCGGCACTGCATGGCCACCGGCGTGCGGGTTGCATCGAGAGAGGTCGGCAGGCGGGCCCCGGCCCGCCTGCCCTGCCGTTGCGTGAAGCGCTGGGCCGCTAGCGGTTGACCAGCTTGGCCGGCAAGGCGATGACCAGGAAGCAGCTGAGGATCAGGCAGCCGGCAAACACCCACAGCGCAGCGTGCGAGGTGCCGG  >  NC_002947_CJ‑RC/4442582‑4442872

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