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 F1 I1 R1	773	79.9	4112934	92.2%	3792125	104.5

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,639,030	C→T	166 (TAG→TAA)	rzpQ ←	Rz‑like protein, Qin prophage

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,639,030	0	C	T	100.0%	93.7 / NA	30	166 (TAG→TAA)	rzpQ	Rz‑like protein, Qin prophage
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (14/16); total (14/16)

TTAAGACCTTTTATCTTACCCTTAAGATTTCAGGAATTTTGGCTCATGGAAGAGTCCTTTTTATTTAAATTTTACATTCCGCGATGTAAATGTTCCGATTTAATATTACCCTACATTTGATGCTTTTTATCTCTTAAAGATTCATAGATCTGTTGACAAGTCACTCCTGCGATGTAGCGTTCGTCAGCAATTTCAGCATAAAGCTGAGCTTCTGCTGCAAT  >  NC_000913/1638920‑1639140

ttAAGACCTTTTATCTTACCCTTAAGATTTCAGGAATTTTGGCTCATGGAAGAGTCCTTTTTATTTAAATTTTACATTCCGCGATGTAAATGTTCCGATTTAATATTACCTTACATTTGATGCTTTTTATCTCTTAAAg                                                                                    >  2:1185025/1‑139 (MQ=255)

 tAAGACCTTTTATCTTACCCTTAAGATTTCAGGAATTTTGGCTCATGGAAGAGTCCTTTTTATTTAAATTTTACATTCCGCGATGTAAATGTTCCGATTTAATATTACCTTACATTTGATGCTTTTTATCTCTTAAAGa                                                                                   >  2:1999826/1‑139 (MQ=255)

    gACCTTTTATCTTACCCTTAAGATTTCAGGAATTTTGGCTCATGGAAGAGTCCTTTTTATTTAAATTTTACATTCCGCGATGTAAATGTTCCGATTTAATATTACCTTACATTTGATGCTTTTTATCTCTTAAAGATTc                                                                                >  1:64477/1‑139 (MQ=255)

         tttATCTTACCCTTAAGATTTCAGGAATTTTGGCTCATGGAAGAGTCCTTTTTATTTAAATTTTACATTCCGCGATGTAAATGTTCCGATTTAATATTACCTTACATTTGATGCTTTTTATCTCTTAAAGATTCATAGa                                                                           >  2:1464399/1‑139 (MQ=255)

          ttATCTTACCCTTAAGATTTCAGGAATTTTGGCTCATGGAAGAGTCCTTTTTATTTAAATTTTACATTCCGCGATGTAAATGTTCCGATTTAATATTACCTTACATTTGATGCTTTTTATCTCTTAAAGATTCATAGAt                                                                          <  1:1999826/139‑1 (MQ=255)

               ttACCCTTAAGATTTCAGGAATTTTGGCTCATGGAAGAGTCCTTTTTATTTAAATTTTACATTCCGCGATGTAAATGTTCCGATTTAATATTACCTTACATTTGATGCTTTTTATCTCTTAAAGATTCATAGATCTGtt                                                                     <  1:1464399/139‑1 (MQ=255)

                 aCCCTTAAGATTTCAGGAATTTTGGCTCATGGAAGAGTCCTTTTTATTTAAATTTTACATTCCGCGATGTAAATGTTCCGATTTAATATTACCTTACATTTGATGCTTTTTATCTCTTAAAg                                                                                    <  1:1437355/122‑1 (MQ=255)

                 aCCCTTAAGATTTCAGGAATTTTGGCTCATGGAAGAGTCCTTTTTATTTAAATTTTACATTCCGCGATGTAAATGTTCCGATTTAATATTACCTTACATTTGATGCTTTTTATCTCTTAAAg                                                                                    >  2:1437355/1‑122 (MQ=255)

                 aCCCTTAAGATTTCAGGAATTTTGGCTCATGGAAGAGTCCTTTTTATTTAAATTTTACATTCCGCGATGTAAATGTTCCGATTTAATATTACCTTACATTTGATGCTTTTTATCTCTTAAAGATTCATAGATCTGTTGa                                                                   <  1:1499713/139‑1 (MQ=255)

                       aaGATTTCAGGAATTTTGGCTCATGGAAGAGTCCTTTTTATTTAAATTTTACATTCCGCGATGTAAATGTTCCGATTTAATATTACCTTACATTTGATGCttttt                                                                                               >  2:2037496/1‑105 (MQ=255)

                       aaGATTTCAGGAATTTTGGCTCATGGAAGAGTCCTTTTTATTTAAATTTTACATTCCGCGATGTAAATGTTCCGATTTAATATTACCTTACATTTGATGCttttt                                                                                               <  1:2037496/105‑1 (MQ=255)

                       aaGATTTCAGGAATTTTGGCTCATGGAAGAGTCCTTTTTATTTAAATTTTACATTCCGCGATGTAAATGTTCCGATTTAATATTACCTTACATTTGATGCTTTTTAt                                                                                             <  2:671441/107‑1 (MQ=255)

                       aaGATTTCAGGAATTTTGGCTCATGGAAGAGTCCTTTTTATTTAAATTTTACATTCCGCGATGTAAATGTTCCGATTTAATATTACCTTACATTTGATGCTTTTTAt                                                                                             >  1:671441/1‑107 (MQ=255)

                       aaGATTTCAGGAATTTTGGCTCATGGAAGAGTCCTTTTTATTTAAATTTTACATTCCGCGATGTAAATGTTCCGATTTAATATTACCTTACATTTGATGCTTTTTATCTCTTAAAGATTCATAGATCTGTTGACAAGTc                                                             >  1:79933/1‑139 (MQ=255)

                              cAGGAATTTTGGCTCATGGAAGAGTCCTTTTTATTTAAATTTTACATTCCGCGATGTAAATGTTCCGATTTAATATTACCTTACATTTGATGCTTTTTATCTCTTa                                                                                       >  2:886443/1‑106 (MQ=255)

                              cAGGAATTTTGGCTCATGGAAGAGTCCTTTTTATTTAAATTTTACATTCCGCGATGTAAATGTTCCGATTTAATATTACCTTACATTTGATGCTTTTTATCTCTTa                                                                                       <  1:886443/106‑1 (MQ=255)

                                            cATGGAAGAGTCCTTTTTATTTAAATTTTACATTCCGCGATGTAAATGTTCCGATTTAATATTACCTTACATTTGATGCTTTTTATCTCTTAAAGATTCATAGATCTGTTGACAAGTCACTCCTGCGATGTAGCGTTCg                                        <  2:64477/139‑1 (MQ=255)

                                               ggAAGAGTCCTTTTTATTTAAATTTTACATTCCGCGATGTAAATGTTCCGATTTAATATTACCTTACATTTGATGCTTTTTATCTCTTAAAGATTCATAGATCTGt                                                                      <  2:1509270/106‑1 (MQ=255)

                                               ggAAGAGTCCTTTTTATTTAAATTTTACATTCCGCGATGTAAATGTTCCGATTTAATATTACCTTACATTTGATGCTTTTTATCTCTTAAAGATTCATAGATCTGt                                                                      >  1:1509270/1‑106 (MQ=255)

                                                      tCCTTTTTATTTAAATTTTACATTCCGCGATGTAAATGTTCCGATTTAATATTACCTTACATTTGATGCTTTTTATCTCTTAAAGATTCATAGATCTGTTGACAAGTCACTCCTGCGATGTAGCGTTCGTCAGCAAttt                              <  2:79933/139‑1 (MQ=255)

                                                           tttatttaAATTTTACATTCCGCGATGTAAATGTTCCGATTTAATATTACCTTACATTTGATGCTTTTTa                                                                                              <  2:1479827/70‑1 (MQ=255)

                                                           tttatttaAATTTTACATTCCGCGATGTAAATGTTCCGATTTAATATTACCTTACATTTGATGCTTTTTa                                                                                              >  1:1479827/1‑70 (MQ=255)

                                                                  aaaTTTTACATTCCGCGATGTAAATGTTCCGATTTAATATTACCTTACATTTGATGCTTTTTATCTCTTAAAGATTCATAGATCTGTTGACAAGTCACTCCTg                                                      >  1:1999302/1‑103 (MQ=255)

                                                                  aaaTTTTACATTCCGCGATGTAAATGTTCCGATTTAATATTACCTTACATTTGATGCTTTTTATCTCTTAAAGATTCATAGATCTGTTGACAAGTCACTCCTg                                                      <  2:1999302/103‑1 (MQ=255)

                                                                            ttCCGCGATGTAAATGTTCCGATTTAACATTACCTTACATTTGATGCTTTTTATCTCTTAAAGATTCATAGATCTGTTGACAAGTCACTCCTGCGATGTAGCGTTCGTCAGCAATTTCAGCATAAAGCTGAGCTTctgc        <  1:1185025/139‑1 (MQ=255)

                                                                               cgcgATGTAAATGTTCCGATTTAATATTACCTTACATTTGATGCTTTTTATCTCTTAAAGATTCATAGATCTGTTGACAAGTCACTCCTGCGATGTAGCGTTCg                                        <  1:1706042/104‑1 (MQ=255)

                                                                               cgcgATGTAAATGTTCCGATTTAATATTACCTTACATTTGATGCTTTTTATCTCTTAAAGATTCATAGATCTGTTGACAAGTCACTCCTGCGATGTAGCGTTCg                                        >  2:1706042/1‑104 (MQ=255)

                                                                                  gATGTAAATGTTCCGATTTAATATTACCTTACATTTGATGCTTTTTATCTCTTAAAGATTCATAGATCTGTTGACAAGTCACTCCTGCGATGTAGCGTTCGTCAGCAATTTCAGCATAAAGCTGAGCTTCTGCTGCAat  <  1:1661289/139‑1 (MQ=255)

                                                                                                 aTTTAATATTACCTTACATTTGATGCTTTTTATCTCTTAAAGATTCATAGATCTGTTGACAAGTCACTCCTGCGATGTAGCGTTCGTCAGCAATTTCAGCATAAAGCTg                 <  2:1645853/109‑1 (MQ=255)

                                                                                                 aTTTAATATTACCTTACATTTGATGCTTTTTATCTCTTAAAGATTCATAGATCTGTTGACAAGTCACTCCTGCGATGTAGCGTTCGTCAGCAATTTCAGCATAAAGCTg                 >  1:1645853/1‑109 (MQ=255)

TTAAGACCTTTTATCTTACCCTTAAGATTTCAGGAATTTTGGCTCATGGAAGAGTCCTTTTTATTTAAATTTTACATTCCGCGATGTAAATGTTCCGATTTAATATTACCCTACATTTGATGCTTTTTATCTCTTAAAGATTCATAGATCTGTTGACAAGTCACTCCTGCGATGTAGCGTTCGTCAGCAATTTCAGCATAAAGCTGAGCTTCTGCTGCAAT  >  NC_000913/1638920‑1639140

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A