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	5,462,375	T→G	18.9%	intergenic (+18/‑22)	PP_4795 → / → holA	lipoprotein/DNA polymerase III subunit delta

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947_CJ‑RC	5,462,375	0	T	G	18.9%	36.9 / 2.5	36	intergenic (+18/‑22)	PP_4795/holA	lipoprotein/DNA polymerase III subunit delta
Reads supporting (aligned to +/- strand): ref base T (11/13); new base G (4/3); total (20/16)
Fisher's exact test for biased strand distribution p-value = 6.85e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.95e-01

ACTGGATGAGCTGCAGCGTAAAGCAGACGAGCGCGCCCAAGCCGAAGCTGCCGCGCTGGAGGCTGCCCGCCGCCAGCAAGCCGAGACGCCTCAGCAATCGCCACTGGAAGTACCGGGCAACTAAGCCCGCGAGGGGCGCCCTCGGGCGCCCCGCCTGTTCCCCATGAAACTCGCCCCCGCCCAACTCAACAAGCACCTGCAAGGCGCCCTGGCACCGGTCTACGTGGTCAGTGGCGACGACCCGCTGCTGTGCCAGGAAGCCGCCGACGCCATCCGCAATGCCGCGCGT  >  NC_002947_CJ‑RC/5462234‑5462522

aCTGGATGAGCTGCAGCGTAAAGCAGACGAGCGCGCCCAAGCCGAAGCTGCCGCGCTGGAGGCTGCCCGCCGCCAGCAAGCCGAGACGCCTCAGCAATCGCCACTGGAAGTACCGGGCAACTAAGTCCGCGAGGGGCGCCCTCGGgcgc                                                                                                                                              >  6:94752/1‑149 (MQ=255)

aCTGGATGAGCTGCAGCGTAAAGCAGACGAGCGCGCCCAAGCCGAAGCTGCCGCGCTGGAGGCTGCCCGCCGCCAGCAAGCCGAGACGCCTCAGCAATCGCCACTGGAAGTACCGGGCAACTAAGCCCGCGAGGGGCGCCCGAGGgcgc                                                                                                                                              <  4:66374/149‑1 (MQ=255)

   ggATGAGCTGCAGCGTAAAGCAGACGAGCGCGCCCAAGCCGAAGCTGCCGCGCTGGAGGCTGCCCGCCGCCAGCAAGCCGAGACGCCTCAGCAATCGCCACTGGAAGTACCGGGCAACTAAGCCCGCGAGGGGCCCCCACCGCCGcccc                                                                                                                                           >  4:170031/1‑149 (MQ=255)

    gATGAGCTGCAGCGTAAAGCAGACGAGCGCGCCCAAGCCGAAGCTGCCGCGCTGGAGGCTGCCCGCCGCCAGCAAGCCGAGACGCCTCACCAATCGCCACTGGAAGTACCGGGCAACTAAGCCCGCGAGGGGCGCCCACCGGCGCCCCg                                                                                                                                          >  8:316495/1‑149 (MQ=255)

      tGAGCTTCAGCGTAAAGCAGACGAGCGCGCCCAAGCCGAAGCTGCCGCGCTGGAGGCTGCCCGCCGCCAGCAAGCCGAGACGCCTCAGCAATCGCCACTGGAAGTACCGGGCAACTAAGCCCGCGAGGGGCGCCCGCCGGCGCcccccc                                                                                                                                        >  1:294614/1‑149 (MQ=255)

        aGCTGCCGCGTAAAGCAGACGAGCGCGCCCAAGCCGAAGCTGCCGCGCGGGAGGCTGCCCGCCGCCAGCAAGCCGAGACGCCTCAGCAATCGCCACTGGAAGTACCGGGCAACTAAGCCCGCGAGGGGCGCCCTCGGGCGCCCCGCCt                                                                                                                                       <  1:103616/148‑1 (MQ=255)

        aGCTGCAGCGTAAATCAGACGAGCGCGCCCAAGCCGAAGCTGCCGCGCTGGAGGCTGCCCGCCGCCAGCAATCCGAGACGCCGCAGCAATCGCCACTGGAAGTACCGGGCAACTAAGCCCGCGAGGGGCGCCCTCGGGCGCCCCGCCt                                                                                                                                       <  5:158194/148‑1 (MQ=255)

                  tAAAGCAGACGAGCGCGCCCAAGCCGAAGCTGCCGCGCTGGAGGCTGCCCGCCGCCAGCAAGCCGAGACGCCTCAGCAATCGCCACTGGAAGTACCGGGCAACTAAGCCCGCGAGGGGCGCCCGCGGGCGCCCCCCCGGTGGCCCATg                                                                                                                             >  7:279086/1‑148 (MQ=255)

                    aaGCAGACGAGCGCGCCCAAGCCGAAGCTGCCGCGCTGGAGGCTGCCCGCCGCCAGCAAGCCGAGACGCCTCAGCAATCGCCACTGGAAGTACCGGGCAACTAAGCCCGCGAGGGGCGCCCTCCGGCCCCCCGCCTGTTGCCCAAGaa                                                                                                                           >  5:95843/1‑148 (MQ=255)

                     aGCAGACGAGCGCGCCCAAGCCGAAGCTGCCGCGCTGGAGGCTGCCCGCCGCCAGCAAGCCGAGACGCCTCAGCAATCGCCACTGGAAGTACCGGGCAACTAAGCCCGCGAGGGGCGCCCTCGGGCGCCCCGCCTGTTCCCCATGAAAc                                                                                                                         <  6:120208/149‑1 (MQ=255)

                     aGCAGACGAGCGCGCCCAAGCCGAAGCTGCCGCGCTGGAGGCTGCCCGCCGCCAGCAAGCCGAGACGCCTCAGCAATCGCCACTGGAAGTACCGGGCAACTAAGCCCGCGAGGGGCGCCCTCGGGCGCCCCGCCGGTTACCCAAGaaa                                                                                                                          >  8:46556/1‑148 (MQ=255)

                                    ccAAGCCGAAGCTGCCGCGCTGGAGGCTGCCCGCCGCCAGCAAGCCGAGACGCCTCAGCAATCGCCACTGGAAGTACCGGGCAACTAAGCCCGCGAGGGGCGCCCGCGGGCGCCCCCCCCGTTGCCCCAGCAACACccccccccccca                                                                                                           >  6:29313/1‑146 (MQ=255)

                                    ccAAGCCGAAGCTGCCGCGCTGGAGGCTGCCCGCCGCCAGCAAGCCGAGACGCCTCAGCAATCGCCACTGGAAGTACCGGGCAACTAAGCCCGCGAGGGGCGCCCACGGGCGCCCCGCCGGGTCCCCATGAAACTCGcccccccgcca                                                                                                           >  2:38215/1‑142 (MQ=255)

                                           gAAGCTGCCGCGCTGGAGGCTGCCCGCCGCCAGCAAGCCGAGACGCCTCAGCAATCGCCACTGGAAGTACCGGGCAACTAAGCCCGCGAGGGGCGCCCTCGGGCGCCCCGCCGGGTGCCCAAGAAACACGCCCCCGCCCCACAcaacaa                                                                                                   >  6:301662/1‑149 (MQ=255)

                                                tGCCGCGCTGGAGGCTGCCCGCCGCCAGCAAGCCGAGACGCCTCAGCAATCGCCACTGGAAGTACCGGGCAACTAAGCCCGCGAGGGGCGCCCGCGGGGGCCCCGCCGGGTGCCCCGGAAAAAAGCCCCCCCCCCACGcaacaaaccc                                                                                               >  1:239137/1‑144 (MQ=255)

                                                     ggcgggAGGCTGCCCGCCGCCAGCAAGCCTAGACGCCTCAGAAATCGCCACTGGGAGTACCGGGCAACAAAGCCCGCGTGGGGCGCCCTCGGGCGCCCCGCCTGTTCCCCATGAAACTCGCCCCCGCCCAACTCAACAAGCACCTGCaa                                                                                         <  4:90320/145‑1 (MQ=255)

                                                            ggCTGCCCGCCGCCAGCAAGCCGAGACGCCTCAGCAATCGCCACTGGAAGTACCGGGCAACTAAGCCCGCGAGGGGGGGCCTCGGGCGCCCCGCCGGTTGCCCCTGTAACTCGCCCCCGCCCCACTCCACAAACACCAGCAAGGCGccc                                                                                  >  5:294316/1‑149 (MQ=255)

                                                                          aGCAAGCCGAGACGCCTCAGCAATCGCCACTGGAAGTACCGGGCAACTAAGCCCGCGAGGGGCGCCCTCGGGCGCCCCGCCTGTTCCCCATGAAACTCGCCCCCGCCCAACTCAACAAGCACCTGCAAGGCGCCCTGGCACCGGTCTAc                                                                    <  5:75988/149‑1 (MQ=255)

                                                                            cAAGCCGAGACGCCTCAGCAATCGCCACTGGAAGTACCGGGCAACTAAGCCCGCGAGGGGCGCCCTCGGGCGCCCCGCCTGTTCCCCATGAAACTCGCCCCCGCCCAACTCAACAAGCACCTGCAAGGCGCCCTGGCACCGGTCTACGt                                                                  <  1:11774/149‑1 (MQ=255)

                                                                               gCCGAGACGCCTCAGCAATCGCCACTGGAAGTACCGGGCAACTAAGCCCGCGAGGGGCGCCCACGGGCGCCCCCCCTGTTCCCCAAGAAACACCCCCCCCCCCAACACAACAACCACCAGCAAGGCCCCCAGGCACCCGTCTACGGGGt                                                               >  2:19964/1‑149 (MQ=255)

                                                                                ccGAGACGCCTCAGCAATCGCCACTGGAAGTCCCGGCCAACAACGCCCGCGTGGGGCGCCCTCGGGCGCCCCGCCTGTTCCCCATGAAACTCGCCCCCGCGCAACTCAACAAGCACCTGCAAGGCGCCCTGGCACCGGTCTACGTGGTc                                                              <  1:38215/149‑1 (MQ=255)

                                                                                 cGAGACCCCCCAGCAAGCCCCACGGGAAGTACCGGCCAACTACCCCCGCGAGGGGCGCCCTCGGGCGCCCCGCCTGTTCCCCATGAAACTCGCCCCCGCCCAACTCAACAAGCACCTGCAAGGCGCCCTGGCACCGGTCTACGTGGTCa                                                             <  1:61991/149‑1 (MQ=255)

                                                                                         cTCAGCAATCGCCACTGGAAGTACGGGGCAACTAAGCCGGCTAGGGGCGCCGTCGGGCGCCCCGCCTGTTCCCCATGAAACTCGCCCCCGCCCAACTCAACAAGCACCTGc                                                                                           <  5:237789/111‑1 (MQ=255)

                                                                                          tCAGCAATCGCCACTGGAAGTACCGGGCAACTAAGCCCGCGAGGGGCGCCCTCGGGCGCCCCGCCAGTTACCCAAGAAACACGCCCCCGCCCAACTCAACAAACACCAGCAAAGCGCCCAGGCACCCGTCTACCTGGTAAGTGGcgac                                                     >  4:259675/1‑148 (MQ=255)

                                                                                                              tACCGGGCAACTACGCCGGCGAGGGGCGCCCTCGGGCGCCCCGCCTGTTCCCCATGAAACTCGCCCCCGCCCAACTCAACAAGCACCTGCAAGGCGCCCTGGCACCGGTCTACGTGGTCAGTGGCGACGACCCGCTGCTGTGCCAGGaa                                <  7:46556/149‑1 (MQ=255)

                                                                                                                ccGGGCAACTAAGCCCGCGAGGGGCGCCCACCGGCGCCCCGCCAGGTGCCCAAGAAAAAAGCCCCCCCCCCACACAAAAACCACCAGCAAGGCGCCCAGGCCCCCGGGTACGTGGGCAGTGGGGCCCACCCCCAGCGGTGGCAGGAAgc                              >  8:200904/1‑149 (MQ=255)

                                                                                                                      aaCTACGCCCGCGAGGGGCGCCCTCGGGCGCCCCGCCTGTTCCCCATGAAACTCGCCCCCGCCCAACTCAACAAGCACCTGCAAGGCGCCCTGGCACCGGTCTACGTGGTCAGTGGCGACGACCCGCTGCTGTGCCAGGAAGCCGCCGa                        <  8:279086/149‑1 (MQ=255)

                                                                                                                        caacgCCCGCGGGGGGCGCCCGGGGCCCCCCCGCCTGTTCCCCATGAAACTCGCCCCCGCCCAACTCAACAAGCACCTGCAAGGCGCCCTGGCACCGGTCTACGTGGTCAGTGGCGACGACCCGCTGCTGTGCCAGGAAGCCGCCGACg                      <  5:94752/145‑1 (MQ=255)

                                                                                                                         aaaGCCCGCGTGGGGCGCCCTCGGCCCCCCCGCCTGTTCCCCATGAAACTCGCCCCCGCCCAACTCAACAAGCACCTGCAAGGCGCCCTGGCACCGGTCTACGTGGTCAGTGGCGACGACCCGCTGCTGTGCCAGGAAGCCGCCGACGc                     <  7:227154/148‑1 (MQ=255)

                                                                                                                             ccggggtggggCGCCCGGGGGCGCCCCGCCTGTTCCCCATGAAACTCGCCCCCGCCCAACTCAACAAGCACCTGCAAGGCGCCCTGGCACCGGTCTACGTGGTCAGTGGCGACGACCCGCTGCTGTGCCAGGAAGCCGCCGACGCCATc                 <  2:124856/142‑1 (MQ=255)

                                                                                                                                       gcgcCCTCGGGCGCCCCGCCTGTTCCCCATGAAACTCGCCCCCGCCCAACTCAACAAGCACCTGCAAGGCGCCCTGGCACCGGTCTACGTGGTCAGTGGCGACGCCCCGCTGCTGTGCCAGGAAGCCCCCGCCGCCATCCGCAATGCcg       >  5:310968/1‑149 (MQ=255)

                                                                                                                                          cccTCGGGCGCCCCGCCTGTTCCCCATGAAACTCGCCCCCGCCCAACTCAACAAGCACCTGCAAGGCGCCCTGGCACCGGTCTACGTGGTCAGTGGCGACGACCCGCTGCTGTGCCAGGAAGCCGCCGACGCCATCCGCAATGCcgcgc    <  2:239137/149‑1 (MQ=255)

                                                                                                                                          cccTCGGGCGCCCCGCCTGTTCCCCATGAAACTCGCCCCCGCCCAACTCAACAAGCACCTGCAAGGCGCCCTGGCACCGGTCTACGTGGTCAGTGGCGACGACCCGCTGCTGTGCCAGGAAGCCGCCGACGCCATCCGCAATGCcgcgc    >  6:120822/1‑149 (MQ=255)

                                                                                                                                          cccTCGGGCGCCCCGCCTGTTCCCCATGAAACTCGCCCCCGCCCAACTCAACAAGCACCTGCAAGGCGCCCTGGCACCGGTCTACGTGGTCAGTGGCGACGACCCGCAGCTGTGCCAGGAAGCCGCCGACGCCATCCGCAATGCcgcgc    >  5:267332/1‑149 (MQ=255)

                                                                                                                                          cccTCGGGCGCCCCGCCTGTTCCCCATGAAACACGCCCCCGCCCAACTCAACAAGCACCTGCAAGGCGCCCTGGCACCGGTCTACGTGGTCAGTGGCGACGACCCGCTGCTGTGCCAGGAAGCCGCCGACGCCATCCGCAATGCcgcgc    >  2:175896/1‑149 (MQ=255)

                                                                                                                                           ccTCGGGCGCCCCGCCTGTTCCCCATGAAACTCGCCCCCGCCCAACTCAACAAGCACCTGCAAGGCGCCCTGGCACCGGTCTACGTGGTCAGTGGCGACGACCCGCTGCTGTGCCAGGAAGCCGCCGACGCCATCCGCAATGCcgcgcg   >  6:243121/1‑149 (MQ=255)

                                                                                                                                             tCGGGCGCCCCGCCTGTTCCCCATGAAACTCGCCCCCGCCCAACTCAACAAGCACCTGCAAGGCGCCCTGGCACCGGTCTACGTGGTCAGTGGCGACGACCCCCTGCTGTGCCAGGAAGCCGCCGACGCCATCCGCAATGCCGCGCGt  >  8:313077/1‑148 (MQ=255)

ACTGGATGAGCTGCAGCGTAAAGCAGACGAGCGCGCCCAAGCCGAAGCTGCCGCGCTGGAGGCTGCCCGCCGCCAGCAAGCCGAGACGCCTCAGCAATCGCCACTGGAAGTACCGGGCAACTAAGCCCGCGAGGGGCGCCCTCGGGCGCCCCGCCTGTTCCCCATGAAACTCGCCCCCGCCCAACTCAACAAGCACCTGCAAGGCGCCCTGGCACCGGTCTACGTGGTCAGTGGCGACGACCCGCTGCTGTGCCAGGAAGCCGCCGACGCCATCCGCAATGCCGCGCGT  >  NC_002947_CJ‑RC/5462234‑5462522

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