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
A9 F48 I1 R1	82	50.4	1709896	99.0%	1692797	139.8

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	249,318	C→A	pseudogene (753/1713 nt)	lfhA ←	flagellar system protein, promoterless fragment

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	249,318	0	C	A	97.4%	129.7 / NA	38	pseudogene (753/1713 nt)	lfhA	flagellar system protein, promoterless fragment
Reads supporting (aligned to +/- strand): ref base C (0/0); major base A (13/24); minor base G (0/1); total (13/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GTTGATGAAAATGGCGTACTGACTGGGCTTAAGGCGGAAGTTTTCCCGAATGCGGATCTCCGGCAGCAGCACGCCGTTGCCGTCAGAAATCACCTGCCGCACGCCGCGAATCCGCTGGGTGAGCGGGTTACCCTGTGCTTTGTCCACCAGCGCCACCAGTTTGTAACCGAGGCTTAAACTGATAGGCTCGATCAGCGGAATGGTTTCCCAACTGACCTGCTGCTCGCTGGTTTCGGTGATGGTGCGGGTCAGCGTTTCGAGG  >  NC_000913/249186‑249447

gTTGATGAAAATGGCGTACTGACTGGGCTTAAGGCGGAAGTTTTCCCGAATGCGGATCTCCGGCAGCAGCACGCCGTTGCCGTCAGAAATCACCTGCCGCACGCCGCGAATCCGCTGGGTGAGCGGGTTACCATGTGCtt                                                                                                                            >  2:466153/1‑140 (MQ=255)

 ttGATGAAAATGGCGTACTGACTGGGCTTAAGGCGGAAGTTTTCCCGAATGCGGATCTCCGGCAGCAGCACGCCGTTGCCGTCAGAAATCACCTGCCGCACGCCGCGAATCCGCTGGGTGAGCGGGTTACCATGTGCttt                                                                                                                           >  1:143531/1‑140 (MQ=255)

              cGTACTGACTGGGCTTAAGGCGGAAGTTTTCCCGAATGCGGATCTCCGGCAGCAGCACGCCGTTGCCGTCAGAAATCACCTGCCGCACGCCGCGAATCCGCTGGGTGAGCGGGTTACCATGTGCTTTGTCCACCAGCGcc                                                                                                              >  1:272949/1‑140 (MQ=255)

              cGTACTGACTGGGCTTAAGGCGGAAGTTTTCCCGAATGCGGATCTCCGGCAGCAGCACGCCGTTGCCGTCAGAAATCACCTGCCGCACGCCGCGAATCCGCTGGGTGAGCGGGTTACCATGTGCTTTGTCCACCAGCGcc                                                                                                              >  1:357527/1‑140 (MQ=255)

                tACTGACTGGGCTTAAGGCGGAAGTTTTCCCGAATGCGGATCTCCGGCAGCAGCACGCCGTTGCCGTCAGAAATCACCTGCCGCACGCCGCGAATCCGCTGGGTGAGCGGGTTACCGTGTGCTTTGTCCACCAGCGccac                                                                                                            <  1:139723/140‑1 (MQ=255)

                tACTGACTGGGCTTAAGGCGGAAGTTTTCCCGAATGCGGATCTCCGGCAGCAGCACGCCGTTGCCGTCAGAAATCACCTGCCGCACGCCGCGAATCCGCTGGGTGAGCGGGTTACCATGTGCTTTGTCCACCAGCGccac                                                                                                            <  1:356405/140‑1 (MQ=255)

                tACTGACTGGGCTTAAGGCGGAAGTTTTCCCGAATGCGGATCTCCGGCAGCAGCACGCCGTTGCCGTCAGAAATCACCTGCCGCACGCCGCGAATCCGCTGGGTGAGCGGGTTACCATGTGCTTTGTCCACCAGCGccac                                                                                                            <  1:683632/140‑1 (MQ=255)

                 actgactgGGCTTAAGGCGGAAGTTTTCCCGAATGCGGATCTCCGGCAGCAGCACGCCGTTGCCGTCAGAAATCACCTGCCGCACGCCGCGAATCCGCTGGGTGAGCGGGTTACCATGTGCTTTGTCCACCAGCGccacc                                                                                                           <  1:521483/140‑1 (MQ=255)

                 actgactgGGCTTAAGGCGGAAGTTTTCCCGAATGCGGATCTCCGGCAGCAGCACGCCGTTGCCGTCAGAAATCACCTGCCGCACGCCGCGAATCCGCTGGGTGAGCGGGTTACCATGTGCTTTGTCCACCAGCGccacc                                                                                                           <  1:664675/140‑1 (MQ=255)

                     actgGGCTTAAGGCGGAAGTTTTCCCGAATGCGGATCTCCGGCAGCAGCACGCCGTTGCCGTCAGAAATCACCTGCCGCACGCCGCGAATCCACTGGGTGAGCGGGTTACCATGTGCTTTGTCCACCAGCGCCACCAGtt                                                                                                       >  2:399560/1‑140 (MQ=255)

                      ctgGGCTTAAGGCGGAAGTTTTCCCGAATGCGGATCTCCGGCAGCAGCACGCCGTTGCCGTCAGAAATCACCTGCCGCACGCCGCGAATCCGCTGGGTGAGCGGGTTACCATGTGCTTTGTCCACCAGCGCCACCAGttt                                                                                                      >  2:77261/1‑140 (MQ=255)

                       tgGGCTTAAGGCGGAAGTTTTCCCGAATGCGGATCTCCGGCAGCAGCACGCCGTTGCCGTCAGAAATCACCTGCCGCACGCCGCGAATCCGCTGGGTGAGCGGGTTACCATGTGCTTTGTCCACCAGCGCCACCAGTTTg                                                                                                     <  2:670342/140‑1 (MQ=255)

                            ttAAGGCGGAAGTTTTCCCGAATGCGGATCTCCGGCAGCAGCACGCCGTTGCCGTCAGAAATCACCTGCCGCACGCCGCGAATCCGCTGGGTGAGCGGGTTACCATGTGCTTTGTCCACCAGCGCCACCAGTTTGTAAcc                                                                                                <  1:689949/140‑1 (MQ=255)

                               aGGCGGAAGTTTTCCCGAATGCGGATCTCCGGCAGCAGCACGCCGTTGCCGTCAGAAATCACCTGCCGCACGCCGCGAATCCGCTGGGTGAGCGGGTTACCATGTGCTTTGTCCACCAGCGCCACCAGTTTGTAACCGAg                                                                                             >  2:127276/1‑140 (MQ=255)

                               aGGCGGAAGTTTTCCCGAATGCGGATCTCCGGCAGCAGCACGCCGTTGCCGTCAGAAATCACCTGCCGCACGCCGCGAATCCGCTGGGTGAGCGGGTTACCATGTGCTTTGTCCACCAGCGCCACCAGTTTGTAACCGAg                                                                                             >  1:633702/1‑140 (MQ=255)

                                    gAAGTTTTCCCGAATGCGGATCTCCGGCAGCAGCACGCCGTTGCCGTCAGAAATCACCTGCCGCACGCCGCGAATCCGCTGGGTGAGCGGGTTACCATGTGCTTTGTCCACCAGCGCCACCAGTTTGTAACCGAGGc                                                                                           >  1:593871/1‑137 (MQ=255)

                                    gAAGTTTTCCCGAATGCGGATCTCCGGCAGCAGCACGCCGTTGCCGTCAGAAATCACCTGCCGCACGCCGCGAATCCGCTGGGTGAGCGGGTTACCATGTGCTTTGTCCACCAGCGCCACCAGTTTGTAACCGAGGc                                                                                           <  2:593871/137‑1 (MQ=255)

                                    gAAGTTTTCCCGAATGCGGATCTCCGGCAGCAGCACGCCGTTGCCGTCAGAAATCACCTGCCGCACGCCGCGAATCCGCTGGGTGAGCGGGTTACCATGTGCTTTGTCCACCAGCGCCACCAGTTTGTAACCGAGGCTTa                                                                                        <  1:77261/140‑1 (MQ=255)

                                     aaGTTTTCCCGAATGCGGATCTCCGGCAGCAGCACGCCGTTGCCGTCAGAAATCACCTGCCGCACGCCGCGAATCCGCTGGGTGAGCGGGTTACCATGTGCTTTGTCCACCAGCGCCACCAGTTTGTAACCGAGGCTTaa                                                                                       <  2:633702/140‑1 (MQ=255)

                                     aaGTTTTCCCGAATGCGGATCTCCGGCAGCAGCACGCCGTTGCCGTCAGAAATCACCTGCCGCACGCCGCGAATCCACTGGGTGAGCGGGTTACCATGTGCTTTGTCCACCAGCGCCACCAGTTTGTAACCGAGGCTTaa                                                                                       <  1:399560/140‑1 (MQ=255)

                                          ttCCCGAATGCGGATCTCCGGCAGCAGCACGCCGTTGCCGTCAGAAATCACCTGCCGCACGCCGCGAATCCGCTGGGTGAGCGGGTTACCATGTGCTTTGTCCACCAGCGCCACCAGTTTGTAACCGAGGCTTAAACTGa                                                                                  <  2:143531/140‑1 (MQ=255)

                                           tCCCGAATGCGGATCTCCGGCAGCAGCACGCCGTTGCCGTCAGAAATCACCTGCCGCACGCCGCGAATCCGCTGGGTGAGCGGGTTACCATGTGCTTTGTCCACCAGCGCCACCAGTTTGTAACCGAGGCTTAAACTGAt                                                                                 >  2:541603/1‑140 (MQ=255)

                                                  tGCGGATCTCCGGCAGCAGCACGCCGTTGCCGTCAGAAATCACCTGCCGCACGCCGCGAATCCGCTGGGTGAGCGGGTTACCATGTGCTTTGTCCACCAGCGCCACCAGTTTGTAACCGAGGCTTAAACTGATAGGCTCg                                                                          <  1:347098/140‑1 (MQ=255)

                                                     ggATCTCCGGCAGCAGCACGCCGTTGCCGTCAGAAATCACCTGCCGCACGCCGCGAATCCGCTGGGTGAGCGGGTTACCATGTGCTTTGTCCACCAGCGCCACCAGTTTGTAACCGAGGCTTAAACTGATAGGCTCGATc                                                                       <  2:387803/140‑1 (MQ=255)

                                                         ctcCGGCAGCAGCACGCCGTTGCCGTCAGAAATCACCTGCCGCACGCCGCGAATCCGCTGGGTGAGCGGGTTACCATGTGCTTTGTCCACCAGCGCCACCAGTTTGTAACCGAGGCTTAAACTGATAGGCTCGATCAGCg                                                                   <  1:466153/140‑1 (MQ=255)

                                                             ggCAGCAGCACGCCGTTGCCGTCAGAAATCACCTGCCGCACGCCGCGAATCCGCTGGGTGAGCGGGTTACCATGTGCTTTGTCCACCAGCGCCACCAGTTTGTAACCGAGGCTTAAACTGATAGGCTCGATCAGCGGAAt                                                               <  2:357527/140‑1 (MQ=255)

                                                                  cagcaCGCCGTTGCCGTCAGAAATCACCTGCCGCACGCCGCGAATCCGCTGGGTGAGCGGGTTACCATGTGCTTTGTCCACCAGCGCCACCAGTTTGTAACCGAGGCTTAAACTGATAGGCTCGATCAGCGGAATGGttt                                                          <  1:298916/140‑1 (MQ=255)

                                                                    gcaCGCCGTTGCCGTCAGAAATCACCTGCCGCACGCCGCGAATCCGCTGGGTGAGCGGGTTACCATGTGCTTTGTCCACCAGCGCCACCAGTTTGTAACCGAGGCTTAAACTGATAGGCTCGATCAGCGGAATGGTTTcc                                                        <  1:7161/140‑1 (MQ=255)

                                                                      aCGCCGTTGCCGTCAGAAATCACCTGCCGCACGCCGCGAATCCGCTGGGTGAGCGGGTTACCATGTGCTTTGTCCACCAGCGCCACCAGTTTGTAACCGAGGCTTAAACTGATAGGCTCGATCAGCGGAATGGTTTCCCa                                                      >  1:548302/1‑140 (MQ=255)

                                                                       cGCCGTTGCCGTCAGAAATCACCTGCCGCACGCCGCGAATCCGCTGGGTGAGCGGGTTACCATGTGCTTTGTCCACCAGCGCCACCAGTTTGTAACCGAGGCTTAAACTGATAGGCTCGATCAGCGGAATGGTTTCCCaa                                                     <  1:797079/140‑1 (MQ=255)

                                                                            ttGCCGTCAGAAATCACCTGCCGCACGCCGCGAATCCGCTGGGTGAGCCGGTTACCATGTGCTTTGTCCACCAGCGCCACCAGTTTGTAACCGAGGCTTAAACTGATAGGCTCGATCAGCGGAATGGTTTCCCAACTGAc                                                >  2:836033/1‑140 (MQ=255)

                                                                                  tCAGAAATCACCTGCCGCACGCCGCGAATCCGCTGGGTGAGCGGGTTACCATGTGCTTTGTCCACCAGCGCCACCAGTTTGTAACCGAGGCTTAAACTGATAGGCTCGATCAGCGGAATGGTTTCCCAACTGACctgctg                                          <  1:592992/140‑1 (MQ=255)

                                                                                        aTCACCTGCCGCACGCCGCGAATCCGCTGGGTGAGCGGGTTACCATGTGCTTTGTCCACCAGCGCCACCAGTTTGTAACCGAGGCTTAAACAGATAGGCTCGATCAGCGGAATGGTTTCCCAACTGACCTGCTGCTCGCt                                    <  1:764015/140‑1 (MQ=255)

                                                                                           aCCTGCCGCACGCCGCGAATCCGCTGGGTGAGCGGGTTACCATGTGCTTTGTCCACCAGCGCCACCAGTTTGTAACCGAGGCTTAAACTGATAGGCTCGATCAGCGGAATGGTTTCCCAACTGACCTGCTGCTCGCTGGt                                 >  1:359038/1‑140 (MQ=255)

                                                                                                   cACGCCGCGAATCCGCTGGGTGAGCGGGTTACCATGTGCTTTGTCCACCAGCGCCACCAGTTTGTAACCGAGGCTTAAACTGATAGGCTCGATCAGCGGAATGGTTTCCCAACTGACCTGCTGCTCGCTGGTTTCGGTGa                         <  2:548302/140‑1 (MQ=255)

                                                                                                        cgcgAATCCGCTGGGTGAGCGGGTTACCATGTGCTTTGTCCACCAGCGCCACCAGTTTGTAACCGAGGCTTAAACTGATAGGCTCGATCAGCGGAATGGTTTCCCAACTGACCTGCTGCTCGCTGGTTTCGGTGATGGTg                    <  2:571089/140‑1 (MQ=255)

                                                                                                               ccGCTGGGTGAGCGGGTTACCATGTGCTTTGTCCACCAGCGCCACCAGTTTGTAACCGAGGCTTAAACTGATAGGCTCGATCAGCGGAATGGTTTCCCAACTGACCTGCTGCTCGCTGGTTTCGGTGATGGTGCGGGTCa             <  2:272949/140‑1 (MQ=255)

                                                                                                                          gCGGGTTACCATGTGCTTTGTCCACCAGCGCCACCAGTTTGTAACCGAGGCTTAAACTGATAGGCTCGATCAGCGGAATGGTTTCCCAACTGACCTGCTGCTCGCTGGTTTCGGTGATGGTGCGGGTCAGCGTTTCGAgg  <  1:541603/140‑1 (MQ=255)

GTTGATGAAAATGGCGTACTGACTGGGCTTAAGGCGGAAGTTTTCCCGAATGCGGATCTCCGGCAGCAGCACGCCGTTGCCGTCAGAAATCACCTGCCGCACGCCGCGAATCCGCTGGGTGAGCGGGTTACCCTGTGCTTTGTCCACCAGCGCCACCAGTTTGTAACCGAGGCTTAAACTGATAGGCTCGATCAGCGGAATGGTTTCCCAACTGACCTGCTGCTCGCTGGTTTCGGTGATGGTGCGGGTCAGCGTTTCGAGG  >  NC_000913/249186‑249447

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A