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
A15 F116 I0 R1	44	26.4	562224	96.5%	542546	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	1,775,556	G→A	47.2%	P323L (CCT→CTT)	clpX ←	S14 family endopeptidase ClpX

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	1,775,556	0	G	A	47.2%	7.8 / 23.4	28	P323L (CCT→CTT)	clpX	S14 family endopeptidase ClpX
Reads supporting (aligned to +/- strand): ref base G (5/9); new base A (4/9); total (9/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.34e-01

AAACCACGCGCACCTGTTTTTCTTTCAATTGCTTTTTCACTAATTGCTGATAAAGCTTCTTCAGTGAACTCTAAATCCACATCATCTAATTCCAGCATTTTAGTATATTGTTTCACAAGTGCATTTTTAGGTTGCGTTAAGATGTTTTTCAACGCAGTTACATCTAATGTTTCTAAATTAGCTACAATTGGCACACGTCCGATAAATTCAGGAATCAAACCATAGGCTTGCAAATCTTCTGGGCGAATTTGTGCTAATAATGCTTGTT  >  CP000730/1775427‑1775694

aatccACGCGAACCTGTTTTTCTTTCAATTTCTTTTTCACTAATTGCTGATAAAGCTTCTTCAGTGAACTCTAAATCCACATCACCTAATTCCAGCATTTTAGTATATTGTTTCACAAGTGCATTTTTAGGTTGCGTTAAg                                                                                                                                 <  2:210471/138‑1 (MQ=255)

    cACGCGCACCTGTTTTTCTTTCAATTTCTTTTTCACTAATTGCTGATAAAGCTTCATCAGTGAACTCTAAATCCACATCATCTAATTCCAGCATTTTAGTATATTGTTTCACAAGTGCATTTTTAAGTTGCGTTAAGATGt                                                                                                                             <  2:246522/141‑1 (MQ=255)

      cgcgCTCCTGTTTTTTTTTCAATTGCTTTTTCACTAATTGCTTATAATGCTTATTCATAGAACTCTCAATCCACTACATCTAATTCCAGCATTTTAGTTTATTGTTGCACAAGTGCATTTTTATGTTTCGTTAAGATGttt                                                                                                                           <  2:13094/141‑1 (MQ=255)

                  tttctttcAATTGCTTTTTCACTAATTGCTGATAAGGCTTCTTCAGTGAACTCTAAATCCACATCATCTAATTCCAGCATTTTAGTATATTGTTTCACAAGTGCATTTTTAGGTTGCGTTAAGATGTTTTTCAACGCAGtt                                                                                                               <  1:253666/141‑1 (MQ=255)

                  tttctttcAATTGCTTTTTCACTAATTGCTGATAAAGCTTCTTCAGTGAACTCTAAATCCACATCATCTAATTCCAGCATTTTAGTATATTGTTTCACAAGTGCATTTTTAGGTTGCGTTGAGATGTTTTTCAACGCAGtt                                                                                                               <  1:170162/141‑1 (MQ=255)

                        tcactggCTTTCTCCCTAGTTGCGTATAATGCTTCTTCAGTGAACTCTAAAGCCTCTTCCTCTAATTCCCGCATTTTTGTATATTGTTTCACAAGTGCATTTTTAAGTTGCGTTAAGATGTTTTTCAACGCAGTTACATCt                                                                                                         <  2:144966/135‑1 (MQ=255)

                         cAATTGCTTTTTCACTAATTGCTGATAAAGCTTCTTCAGTGAACTCTAAATCCACATCATCTAATTCCAGCATTTTAGTATATTGTTTCACAAGTGCATTTTTAGGTTGCGTTAAGATGTTTTTCAACGCAGTTACATCTa                                                                                                        <  2:64293/141‑1 (MQ=255)

                                                    aaGCTTCTTCAGTGAACTCTAAATCCACATCATCTAATTCCAGCATTTTAGTATATTGTTTCACAAGTGCATTTTTAGGTTGCGTTAAGATGTTTTTCAACGCAGTTACATCTAATGTTTCTAAATTAGCTACAATTGGcc                                                                             >  1:18681/1‑140 (MQ=255)

                                                                    ctctAAATCCACATCATCTAATTCCAGCATTTTAGTATATTGTTTCACAAGTGCATTTTTAGGTTGCGTTAAGATGTTTTTCAACGCAGTTACATCTAATGTTTCTAAATTAGCTACAATTGGCACACGTCCGATAAATTc                                                             >  2:233814/1‑141 (MQ=255)

                                                                      ctAAATCCACATCATCTAATTCCAGCATTTTAGTATATTGTTTCACAAGTGCATTTTTAAGTTGCGTTAAGATGTTTTTCAACGCAGTTACATCTAATGTTTCTAAATTAGCTACAATTGGCACACGTCCGATAAATTCAg                                                           <  2:272978/141‑1 (MQ=255)

                                                                            ccACATCATCTAATCCCAGCATTTTAGTATATTGTTTCACAAGTGCATTTTTAGGTTGCGTTAAGATGTTTTTCAACGCAGTTACATCTAATGTTTCTAAATTAGCTACAATTGGCACACGTCCGATAAATTCAGGAATCa                                                     <  1:176681/141‑1 (MQ=255)

                                                                               catcatCTAATTCCAGCATTTTAGTATATTGTTTCACAAGTGCATTTTTAAGTTGCGTTAAGATGTTTTTCAACGCAGTTTCATCTAATGTTTCTAAATTCGCTACAATTGGCACCCGTCCGCTAATTTCTGGAATCAAAc                                                  >  2:20348/1‑141 (MQ=255)

                                                                               catcatCTAATTCCAGCATTTTAGTATATTGTTTCACAAGTGCATTTTTAAGTTGCGTTAAGATGTGTTTCAACGCAGTTACATCTAATGTTTCTAAATTAGCTACAATTGGCACACGTCCGATAAATTCAGGAATCAAAc                                                  <  1:14248/141‑1 (MQ=255)

                                                                                    tcTAATTCCAGCATTTTAGTATATTGTTTCACAAGTGGATTTTTAAGTTGCGTTAAGATGTTTTTCAACGCAGTTAGATCTAATGTTTCTAAATTAGCTACATTTGGCACACGGCGGATAAATTTAGGAATCAAACCATAg                                             >  2:215568/1‑141 (MQ=255)

                                                                                         ttCCAGCATTTTAGTATATTGTTTCACAAGTGCATTTTTAAGTTGCGTTAAGATGTTTTTCAACGCAGTTACATCTAATGTTTCTAAATTAGCTACAATTGGCACACGTCCGATAAATTCAGGAATCAAACCATAGGCTTg                                        >  1:217775/1‑141 (MQ=255)

                                                                                              gCATTTTAGTATATTGTTTCACAAGTGCATTTTTAGTTTGCGTTAAGATGTTTTTCAACGCAGTTACATCTAATGTTTCTAAATTAGCTACAATTGGCACACGTCCGCTAAATTCAGGACTCAAACCATAGGCTTGCAAAt                                   >  1:236254/1‑141 (MQ=255)

                                                                                                       tttatTGTTTCACAAGTGCATTTTTAGGTTGCGTTAAGATGTTTTTCAACGCAGTTACATCTAATGTTTCTAAATTAGCTACAATTGGCACACGTCCGATAAATTCAGGAATCAAACCATAGGCTTGCAAATCTTCTGGGc                          <  1:209945/139‑1 (MQ=255)

                                                                                                       tataTTGTTTCACAAGTGCATTTTGAAGTTGCGTTAAGATGTTTTTCAACGCAGTTACATCTAATGTTTCTAAATTAGCTACAATTGGCACACGTCCGATAAATTCAGGAATCAAACCATAGGCTTGCAAATCTTCTGGGc                          <  2:80818/141‑1 (MQ=255)

                                                                                                        atatTGTTTCACAAGTGCATTTTTAAGTTGCGTTAAGATGTTTTTCAACGCAGTTAAATCTAATGTTTCTCAATTAGCTACATTTGGCACACGTCCGATAAATTCAGGAATCAAACCATAGGATTGCAAGTCTTCTGGGCg                         >  2:279471/1‑141 (MQ=255)

                                                                                                                tCACAAGTGCATTTTTAAGTTGCGTTAAGATGTTTTTCAACGCAGTTACATCTAATGTTTCTAAATTAGCTACAATTGGCACACGTCCGATAAATTCAGGAATCAAACCATAGGCTTGCAAATCTTCTGGGCGTATTtgtg                 <  1:174860/141‑1 (MQ=255)

                                                                                                                tCACAAGTGCATTTTTAAGTTGCGTTAAGATGTTTTTCAACGCAGTTACATCTAATGTTTCTAAATTAGCTACAATTGGCACACGTCCGATAAATTCAGGAATCAAACCATAGGCTTGCAAATCTTCTGGGCGAATTtgtg                 <  1:23593/141‑1 (MQ=255)

                                                                                                                tCACAAGTGCATTCTTAAGTTGCGGTAAGATGTTTTTCAACGCAGTTACATCTAATGTTTCTAAATTAGCTACAATTGGCACACGTCCGATAAATTCAGGAATCAAACCATAGGCTTGCAAATCTTCTGGGCGCATTtgtg                 <  1:174835/141‑1 (MQ=255)

                                                                                                                   caAGTGCATTTTTAAGTTGCGTTAAGATGTTTTTCAACGCAGTTACATCTAATGTTTCTAAATTAGCTACAATTGGCACACGTCCGATAAATTCAGGAATCAAACCATAGGCTTGCAAATCTTCTGGGCGAATTTGTGCta              <  1:71612/141‑1 (MQ=255)

                                                                                                                       gtcgtttttAGGTTGCGTTAAGATGGTTTTCAACGCAGTTACATCTAATGTTTCTAAATTAGCTACAATTGGCACACGTCCGATAAATTCAGGAATCAAACCATAGGCTTGCAAATCTTCTGGGCGAATTTGTGCtaataa          <  2:68907/137‑1 (MQ=255)

                                                                                                                         cttttttAGGTTGCGTTAAGATGTTGTTCAACGGAGTTACACCTAATGTTTCTAAATTAGCTACAATTGGCACACGTCAGATAAATTCAGGAATCAAACCATAGGCTTGCAAATCATATGGTCGAATGTGTGCTAATAATg        <  2:60682/139‑1 (MQ=255)

                                                                                                                            ttttAGGTTGCGTTAAGATGTTTTTCAACGCAGTTACATCTAATGTTTCTAAATTAGCTACAATTGGCACACGTCCGATAAATTCAGGAATCAAACCATAGGCTTGCAAATCTTCTGGGCGAATTTGTGCTAATAATGCtt     <  1:27294/141‑1 (MQ=255)

                                                                                                                             tttAGGTTGCGTTAAGATGTTTTTCAACGCAGTTACATCTAATGTTTCTAAATTAGCTACAATTGGCACACGTCCGATAAATTCAGGAATCAAACCATAGGCTTGCAAATCTTCTGGGCGAATTTGTGCTAATAATGCttt    >  1:159386/1‑140 (MQ=255)

                                                                                                                               tAGGTTGCGTTAAGATGTTTTTCAACGCAGTTACATCTAATGTTTCTAAATTAGCTACAATTGGCACACGTCCGATAAATTCAGGAATCAAACCATAGGCTTGCAAATCTTCTGGGCGAATTTGTGCTAATAATGCTTGtt  >  1:3661/1‑141 (MQ=255)

AAACCACGCGCACCTGTTTTTCTTTCAATTGCTTTTTCACTAATTGCTGATAAAGCTTCTTCAGTGAACTCTAAATCCACATCATCTAATTCCAGCATTTTAGTATATTGTTTCACAAGTGCATTTTTAGGTTGCGTTAAGATGTTTTTCAACGCAGTTACATCTAATGTTTCTAAATTAGCTACAATTGGCACACGTCCGATAAATTCAGGAATCAAACCATAGGCTTGCAAATCTTCTGGGCGAATTTGTGCTAATAATGCTTGTT  >  CP000730/1775427‑1775694

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A