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
A8 F1 I1 R1	771	44.8	2153074	94.1%	2026042	109.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,892,455	G→A	A281T (GCG→ACG)	mdtL →	multidrug efflux system protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,892,455	0	G	A	100.0%	144.5 / NA	45	A281T (GCG→ACG)	mdtL	multidrug efflux system protein
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (22/23); total (22/23)

AATACGCCACCATTATGGCGCTGACCGCTGGCGTCAGCATGACCGTTTCATTCTCCACGCCATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGGCGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGTAGGTTTTGGTGTGGCGATGAGTCAGGCGTTAGGGCCGTTTTCATTACGCGCGGGCG  >  NC_000913/3892330‑3892590

aaTACGCCACCATTATGGCGCTGACCGCTGGCGTCAGCATGACCGTTTCATTCTCCACGCCATTTGCGCTGGGAATTTTTAAGCCACGCACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCActct                                                                                                                            <  2:984571/139‑1 (MQ=255)

 aTACGCCACCATTATGGCGCTGACCGCTGGCGTCAGCATGACCGTTTCATTCTCCACGCCATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCtt                                                                                                                           <  1:680562/139‑1 (MQ=255)

 aTACGCCACCATTATGGCGCTGACCGCTGGCGTCAGCATGACCGTTTCATTCTCCACGCCATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCtt                                                                                                                           <  1:301995/139‑1 (MQ=255)

          caTTATGGCGCTGACCGCTGGCGTCAGCATGACCGTTTCATTCTCCACGCCATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCa                                                                                                                  >  2:646377/1‑139 (MQ=255)

          caTTATGGCGCTGACCGCTGGCGTCAGCATGACCGTTTCATTCTCCACGCCATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCa                                                                                                                  >  1:184215/1‑139 (MQ=255)

          caTTATGGCGCTGACCGCTGGCGTCAGCATGACCGTTTCATTCTCCACGCCATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCa                                                                                                                  >  1:481870/1‑139 (MQ=255)

                   gcTGACCGCTGGCGTCAGCATGACCGTTTCATTCTCCACGCCATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCAt                                                                                                         >  1:91962/1‑139 (MQ=255)

                       aCCGCTGGCGTCAGCATGACCGTTTCATTCTCCACGCCATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGgcgacg                                                                                                                                       >  2:338566/1‑105 (MQ=255)

                       aCCGCTGGCGTCAGCATGACCGTTTCATTCTCCACGCCATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCgg                                                                                                     <  2:601392/139‑1 (MQ=255)

                          gCTGGCGTCAGCATGACCGTTTCATTCTCCACGCCATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGttt                                                                                                  <  2:91962/139‑1 (MQ=255)

                            tGGCGTCAGCATGACCGTTTCATTCTCCACGCCATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTtct                                                                                                <  2:481870/139‑1 (MQ=255)

                            tGGCGTCAGCATGACCGTTTCATTCTCCACGCCATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTtct                                                                                                >  2:1040779/1‑139 (MQ=255)

                              gCGTCAGCATGACCGTTTCATTCTCCACGCCATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTctct                                                                                              <  1:493106/139‑1 (MQ=255)

                                      aTGACCGTTTCATTCTCCACGCCATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTa                                                                                      <  2:598514/139‑1 (MQ=255)

                                       tGACCGTTTCATTCTCCACGCCATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTAt                                                                                     <  2:80673/139‑1 (MQ=255)

                                        gACCGTTTCATTCTCCACGCCATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATc                                                                                    >  1:792002/1‑139 (MQ=255)

                                                          gCCATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTtct                                                                                                <  2:144002/109‑1 (MQ=255)

                                                          gCCATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTtct                                                                                                >  1:144002/1‑109 (MQ=255)

                                                               ttGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGtt                                                                                                                     >  1:77527/1‑83 (MQ=255)

                                                               ttGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGtt                                                                                                                     <  2:77527/83‑1 (MQ=255)

                                                                  cgcTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGt                                                          <  2:792002/139‑1 (MQ=255)

                                                                    cTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGTAg                                                        >  1:448259/1‑139 (MQ=255)

                                                                      gggAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGAt                                                                                                                                  <  1:808879/63‑1 (MQ=255)

                                                                      gggAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGAt                                                                                                                                  >  2:808879/1‑63 (MQ=255)

                                                                            ttttAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGTAGGTTTTGgt                                                <  1:333670/139‑1 (MQ=255)

                                                                                 aGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGTAGGTTTTGGTGTGGc                                           >  1:401755/1‑139 (MQ=255)

                                                                                 aGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTACCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGTAGGTTTTGGTGTGGc                                           >  2:197051/1‑139 (MQ=255)

                                                                                   ccACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGTAGGTTTTGGTGTGGCGa                                         <  2:401755/139‑1 (MQ=255)

                                                                                                 gatCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGTAGGttt                                                    <  1:313754/114‑1 (MQ=255)

                                                                                                 gatCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGTAGGttt                                                    >  2:313754/1‑114 (MQ=255)

                                                                                                 gatCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCAGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGt                                                          >  1:859092/1‑108 (MQ=255)

                                                                                                 gatCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCAGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGt                                                          <  2:859092/108‑1 (MQ=255)

                                                                                                  atCACCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGTAGGTTTTGGTGTGGCGATGAGTCAGGCGTTAg                          >  1:205775/1‑139 (MQ=255)

                                                                                                     aCCTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGTAGGTTTTGGTGTGGCGATGAGTCAGGCGTTAGGGc                       >  2:737376/1‑139 (MQ=255)

                                                                                                       cTCGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTACCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGTAGGTTTTGGTGTGGCGATGAGTCAGGCGTTAGGGCCg                     <  1:197051/139‑1 (MQ=255)

                                                                                                         cGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGt                                                          <  2:28863/100‑1 (MQ=255)

                                                                                                         cGCAGGTGTTATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGt                                                          >  1:28863/1‑100 (MQ=255)

                                                                                                                 ttATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTa                                                                                      >  2:345423/1‑64 (MQ=255)

                                                                                                                 ttATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTa                                                                                      <  1:345423/64‑1 (MQ=255)

                                                                                                                 ttATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGTAGGTTTTGGTGTGGCGATg                                       >  2:740694/1‑111 (MQ=255)

                                                                                                                 ttATTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGTAGGTTTTGGTGTGGCGATg                                       <  1:740694/111‑1 (MQ=255)

                                                                                                                   aTTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGt                                                          >  2:1011722/1‑90 (MQ=255)

                                                                                                                   aTTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGt                                                          <  1:1011722/90‑1 (MQ=255)

                                                                                                                   aTTCCTGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGTAGGTTTTGGTGTGGCGATGAGTCAGGCGTTAGGGCCGTTTTCATTAcgc         >  2:131280/1‑139 (MQ=255)

                                                                                                                        tGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGTAGGTTTTGGTGTGGCGATGAGTCAGGCGTTAGGGCCGTTTTCATTACGCGCggg    >  2:857387/1‑139 (MQ=255)

                                                                                                                        tGGCGACGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGTAGGTTTTGGTGTGGCGATGAGTCAGGCGTTAGGGCCGTTTTCATTACGCGCggg    <  1:646377/139‑1 (MQ=255)

                                                                                                                         ggcgacGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGt                                                          >  2:516869/1‑84 (MQ=255)

                                                                                                                         ggcgacGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGt                                                          <  1:516869/84‑1 (MQ=255)

                                                                                                                         ggcgacGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGTAGGTTTTGgtgt                                              >  2:692393/1‑96 (MQ=255)

                                                                                                                         ggcgacGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGTAGGTTTTGgtgt                                              <  1:692393/96‑1 (MQ=255)

                                                                                                                         ggcgacGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGTAGGTTTTGGTGTGGCGATGAGTCAGGCGTTAGGGCCGTTTTCATTACGCGCGGGc   >  1:836606/1‑139 (MQ=255)

                                                                                                                          gcgacgGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGTAGGTTTTGGTGTGGCGATGAGTCAGGCGTTAGGGCCGTTTTCATTACGCGCGGGCg  >  1:348613/1‑139 (MQ=255)

AATACGCCACCATTATGGCGCTGACCGCTGGCGTCAGCATGACCGTTTCATTCTCCACGCCATTTGCGCTGGGAATTTTTAAGCCACGTACGTTGATGATCACCTCGCAGGTGTTATTCCTGGCGGCGGGGATCACTCTTGCCGTTTCACCTTCCCATGCGGTTTCTCTGTTTGGTATCACGCTGATTTGCGCCGGTTTCTCGGTAGGTTTTGGTGTGGCGATGAGTCAGGCGTTAGGGCCGTTTTCATTACGCGCGGGCG  >  NC_000913/3892330‑3892590

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