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
A4 F1 I2 R1	780	68.3	3343050	93.5%	3125751	102.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,673,117	C→T	W11* (TGG→TGA)	mdtI ←	multidrug efflux system transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,673,117	0	C	T	100.0%	150.2 / NA	47	W11* (TGG→TGA)	mdtI	multidrug efflux system transporter
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (23/24); total (23/24)

CTTGAGAAAGCGCACTAAAGGCAGCCAGCACCGCCGCCAGGGAGAGCAAGCCAAATATTTTGCGACGAAAGCCGTCAGAAAATTTCAAAAAGACGTTAGCAACGATTTCCAGCACGATTGCCAATGCCAGCCAGGCGGCGTGAACCCATTCAAACTGCGCCATGGTTCACCTCCAGTTCAGGTTTACGCGCTTTACGGGTACCTGATTTTATCAACACAATCCCGGCGACCAGGGTGGTTAACCCGGCAATTTTCA  >  NC_000913/1672987‑1673242

cTTGAGAAAGCGCACTAAAGGCAGCCAGCACCGCCGCCAGGGAGAGCAAGCCAAATATTTTGCGACGAAAGCCGTCAGAAAATTTCAAAAAGACGTTAGCAACGATTTCCAGCACGATTGCCAATGCCAGTCAggcggc                                                                                                                       >  1:270885/1‑139 (MQ=255)

cTTGAGAAAGCGCACTAAAGGCAGCCAGCACCGCCGCCAGGGAGAGCAAGCCAAATATTTTGCGACGAAAGCCGTCAGAAAATTTCAAAAAGACGTTAGCAACGATTTCCAGCACGATTGCCAATGCCAGTCAggcggc                                                                                                                       >  1:1578250/1‑139 (MQ=255)

  tGAGAAAGCGCACTAAAGGCAGCCAGCACCGCCGCCAGGGAGAGCAAGCCAAATATTTTGCGACGAAAGCCGTCAGAAAATTTCAAAAAGACGTTAGCAACGATTTCCAGCACGATTGCCAATGCCAGTCAGGCGGCGt                                                                                                                     >  1:335006/1‑139 (MQ=255)

     gaAAGCGCACTAAAGGCAGCCAGCACCGCCGCCAGGGAGAGCAAGCCAAATATTTTGCGACGAAAGCCGTCAGAAAATTTCAAAAAGACGTTAGGAACGATTTCCAGCACGATTGCCAATGCCAGTCAGGCGGCGTGaa                                                                                                                  <  1:1181569/139‑1 (MQ=255)

          cgcACTAAAGGCAGCCAGCACCGCCGCCAGGGAGAGCAAGCCAAATATTTTGCGACGAAAGCCGTCAGAAAATTTCAAAAAGACGTTAGCAACGATTTCCAGCACGATTGCCAATGCCAGTCAGGCGGCGTGAACCCAt                                                                                                             >  2:1549242/1‑139 (MQ=255)

                       gccagcACCGCCGCCAGGGAGAGCAAGCCAAATATTTTGCGACGAAAGCCGTCAGAAAATTTCAAAAAGACGTTAGCAACGATTTCCAGCACGATTGCCAATGCCAGTCAgg                                                                                                                           >  2:1280115/1‑112 (MQ=255)

                       gccagcACCGCCGCCAGGGAGAGCAAGCCAAATATTTTGCGACGAAAGCCGTCAGAAAATTTCAAAAAGACGTTAGCAACGATTTCCAGCACGATTGCCAATGCCAGTCAgg                                                                                                                           <  1:1280115/112‑1 (MQ=255)

                        ccagcACCGCCGCCAGGGAGAGCAAGCCAAATATTTTGCGACGAAAGCCGTCAGAAAATTTCAAAAAGACGTTAGCAACGATTTCCAGCACGATTGCCAATGCCAGTCAGGCGGCGTGAACCCATTCAAACTGCGCCAt                                                                                               <  2:270885/139‑1 (MQ=255)

                         cagcACCGCCGCCAGGGAGAGCAAGCCAAATATTTTGCGACGAAAGCCGTCAGAAAATTTCAAAAAGACGTTAGCAACGATTTCCAGCACGATTGCCAATGCCAGTCAGGCGGCGTGAACCCATTCAAACTGCGCCATg                                                                                              >  2:1333495/1‑139 (MQ=255)

                         cagcACCGCCGCCAGGGAGAGCAAGCCAAATATTTTGCGACGAAAGCCGTCAGAAAATTTCAAAAAGACGTTAGCAACGATTTCCAGCACGATTGCCAATGCCAGTCAGGCGGCGTGAACCCATTCAAACTGCGCCATg                                                                                              >  2:468410/1‑139 (MQ=255)

                                 ccgccAGGGAGAGCAAGCCAAATATTTTGCGACGAAAGCCGTCAGAAAATTTCAAAAAGACGTTAGCAACGATTTCCAGCACGATTGCCAATGCCAGTCAGGCGGCGTGAACCCATTCAAACTGCGCCATGGTTCACCt                                                                                      >  2:75934/1‑139 (MQ=255)

                                            agCAAGCCAAATATTTTGCGACGAAAGCCGTCAGAAAATTTCAAAAAGACGTTAGCAACGATTTCCAGCACGATTGCCAATGCCAGTCAGGCGGCGTg                                                                                                                    <  1:1305874/98‑1 (MQ=255)

                                            agCAAGCCAAATATTTTGCGACGAAAGCCGTCAGAAAATTTCAAAAAGACGTTAGCAACGATTTCCAGCACGATTGCCAATGCCAGTCAGGCGGCGTg                                                                                                                    >  2:1305874/1‑98 (MQ=255)

                                            agCAAGCCAAATATTTTGCGACGAAAGCCGTCAGAAAATTTCAAAAAGACGTTAGCAACGATTTCCAGCACGATTGCCAATGCCAGTCAGGCGGCGTg                                                                                                                    <  2:1436095/98‑1 (MQ=255)

                                            agCAAGCCAAATATTTTGCGACGAAAGCCGTCAGAAAATTTCAAAAAGACGTTAGCAACGATTTCCAGCACGATTGCCAATGCCAGTCAGGCGGCGTg                                                                                                                    >  1:1436095/1‑98 (MQ=255)

                                               aaGCCAAATATTTTGCGACGAAAGCCGTCAGAAAATTTCAAAAAGACGTTAGCAACGATTTCCAGCACGATTGCCAATGCCAGTCAGGCGGCGTGAACCCATTCAAACTGCGCCATGGTTCACCTCCAGTTCAGGTTTa                                                                        <  1:1333495/139‑1 (MQ=255)

                                                 gCCAAATATTTTGCGACGAAAGCCGTCAGAAAATTTCAAAAAGACGTTAGCAACGATTTCCAGCACGATTGCCAATGCCAGTCAGGCGGCGTGAACCCATTCAAACTGCGCCATGGTTCACCTCCAGTTCAGGTTTAcg                                                                      >  1:1377175/1‑139 (MQ=255)

                                                 gCCAAATATTTTGCGACGAAAGCCGTCAGAAAATTTCAAAAAGACGTTAGCAACGATTTCCAGCACGATTGCCAATGCCAGTCAGGCGGCGTGAACCCATTCAAACTGCGCCATGGTTCACCTCCAGTTCAGGTTTAcg                                                                      <  2:1578250/139‑1 (MQ=255)

                                                 gCCAAATATTTTGCGACGAAAGCCGTCAGAAAATTTCAAAAAGACGTTAGCAACGATTTCCAGCACGATTGCCAATGCCAGTCAGGCGGCGTGAACCCATTCAAACTGCGCCATGGTTCACCTCCAGTTCAGGTTTAcg                                                                      <  2:1377175/139‑1 (MQ=255)

                                                    aaaTATTTTGCGACGAAAGCCGTCAGAAAATTTCAAAAAGACGTTAGCAACGATTTCCAGCACGATTGCCAATGCCAGTCAGGCGGCGTGAACCCATTCAAACTGCGCCATGGTTCACCTCCAGTTCAGGTTTACgcgc                                                                   <  1:75934/139‑1 (MQ=255)

                                                       tatTTTGCGACGAAAGCCGTCAGAAAATTTCAAAAAGACGTTAGCAACGATTTCCAGCACGATTGCCAATGCCAGTCAGGCGGCGTGAACCCATTCAAACTGCGCCATGGTTCACCTCCAGTTCAGGTTTACGCGCttt                                                                <  1:1549242/139‑1 (MQ=255)

                                                           ttGCGACGAAAGCCGTCAGAAAATTTCAAAAAGACGTTAGCAACGATTTCCAGCACGATTGCCAATGCCAGTCAGGCGGCGTGAACCCATTCAAACTGCGCCATGGTTCACCTCCAGTTCAGGTTTACGCGCTTTACgg                                                            >  1:1395026/1‑139 (MQ=255)

                                                               gacgaAAGCCGTCAGAAAATTTCAAAAAGACGTTAGCAACGATTTCCAGCACGATTGCCAATGCCAGTCAGGCGGCGTGAACCCATTCAAACTGCGCCATGGTTCACCTCCAGTTCAGGTTTACGCGCTTTACGGGTAc                                                        <  1:468410/139‑1 (MQ=255)

                                                               gacgaAAGCCGTCAGAAAATTTCAAAAAGACGTTAGCAACGATTTCCAGCACGATTGCCAATGCCAGTCAGGCGGCGTGAACCCATTCAAACTGCGCCATGGTTCACCTCCAGTTCAGGTTTACGCGCTTTACGGGTAc                                                        <  2:1395026/139‑1 (MQ=255)

                                                               gacgaAAGCCGTCAGAAAATTTCAAAAAGACGTTAGCAACGATTTCCAGCACGATTGCCAATGCCAGTCAGGCGGCGTGAACCCATTCAAACTGCGCCATGGTTCACCTCCAGTTCAGGTTTACGCGCTTTACGGGTAc                                                        <  2:356651/139‑1 (MQ=255)

                                                                   aaaGCCGTCAGAAAATTTCAAAAAGACGTTAGCAACGATTTCCAGCACGATTGCCAATGCCAGTCAGGCGGCGTGAACCCATTCAAACTGCGCCATGGTTCACCTCCAGTTCAGGTTTACGCGCTTTACGGGTACCTGa                                                    >  2:1555413/1‑139 (MQ=255)

                                                                          tCAGAAAATTTCAAAAAGACGTTAGCAACGATTTCCAGCACGATTGCCAATGCCAGTCAGGCGGCGTGaa                                                                                                                  >  1:762693/1‑70 (MQ=255)

                                                                          tCAGAAAATTTCAAAAAGACGTTAGCAACGATTTCCAGCACGATTGCCAATGCCAGTCAGGCGGCGTGaa                                                                                                                  <  2:762693/70‑1 (MQ=255)

                                                                                   ttCAAAAAGACGTTAGCAACGATTTCCAGCACGATTGCCAATGCCAGTCAGGCGGCGTGAACCCATTCAAACTGCGCCATGGTTCACCTCCAGTTCAGGTTTACGCGCTTTACGGGTAc                                                        >  1:573977/1‑119 (MQ=255)

                                                                                   ttCAAAAAGACGTTAGCAACGATTTCCAGCACGATTGCCAATGCCAGTCAGGCGGCGTGAACCCATTCAAACTGCGCCATGGTTCACCTCCAGTTCAGGTTTACGCGCTTTACGGGTAc                                                        <  2:573977/119‑1 (MQ=255)

                                                                                      aaaaaGACGTTAGCAACGATTTCCAGCACGATTGCCAATGCCAGTCAGGCGGCGTGAACCCATTCAAACTGCGCCATGGTTCACCTCCAGTTCAGGTTTACGCGCTTTACGGGTACCTGATTTTATCAACACAATCCCg                                 <  1:1022961/139‑1 (MQ=255)

                                                                                      aaaaaGACGTTAGCAACGATTTCCAGCACGATTGCCAATGCCAGTCAGGCGGCGTGAACCCATTCAAACTGCGCCATGGTTCACCTCCAGTTCAGGTTTACGCGCTTTACGGGTACCTGATTTTATCAACACAATCCCg                                 <  1:1555413/139‑1 (MQ=255)

                                                                                        aaaGACGTTAGCAACGATTTCCAGCACGATTGCCAATGCCAGTCAGGCGGCGTGAACCCATTCAAACTGCGCCATGGTTc                                                                                          >  2:1310371/1‑80 (MQ=255)

                                                                                        aaaGACGTTAGCAACGATTTCCAGCACGATTGCCAATGCCAGTCAGGCGGCGTGAACCCATTCAAACTGCGCCATGGTTc                                                                                          <  1:1310371/80‑1 (MQ=255)

                                                                                            aCGTTAGCAACGATTTCCAGCACGATTGCCAATGCCAGTCAGGCGGCGTGAACCCATTCCAACTGCGCCATGGTTCACCTCCAGTTCAGGTTTAcg                                                                      <  2:352590/96‑1 (MQ=255)

                                                                                            aCGTTAGCAACGATTTCCAGCACGATTGCCAATGCCAGTCAGGCGGCGTGAACCCATTCAAACTGCGCCATGGTTCACCTCCAGTTCAGGTTTAcg                                                                      >  1:352590/1‑96 (MQ=255)

                                                                                                      cGATTTCCAGCACGATTGCCAATGCCAGTCAGGCGGCGTGAACCCATTCAAACTGCGCCATGGTTCACCTCCAGTTCAGGTTTAcg                                                                      <  1:747525/86‑1 (MQ=255)

                                                                                                      cGATTTCCAGCACGATTGCCAATGCCAGTCAGGCGGCGTGAACCCATTCAAACTGCGCCATGGTTCACCTCCAGTTCAGGTTTAcg                                                                      >  2:747525/1‑86 (MQ=255)

                                                                                                           tcaaGCACGATAGCCAATGCCAGTCAGGCGGCGTGAACCCATTCAAACTGCGCCATGGTTc                                                                                          >  1:970495/4‑61 (MQ=255)

                                                                                                           tCCAGCACGATTGCCAATGCCAGTCAGGCGGCGTGAACCCATTCAAACTGCGCCATGGTTc                                                                                          <  2:970495/61‑1 (MQ=255)

                                                                                                                 aCGATTGCCAATGCCAGTCAGGCGGCGTGTACCCATTCAAACTGCGCCATGGTTCACCTCCAGTTCAGGTTTAc                                                                       <  1:1184194/74‑1 (MQ=255)

                                                                                                                 aCGATTGCCAATGCCAGTCAGGCGGCGTGAACCCATTCAAACTGCGCCATGGTTCACCTCCAGTTCAGGTTTAc                                                                       >  2:1184194/1‑74 (MQ=255)

                                                                                                                  cGATTGCCAATGCCAGTCAGGCGGCGTGAACCCATTCAAACTGCGCCATGGTTCACCTCCAGTTCAGGTTTACGCGCTTTACGGGTACCTGATTTTATCAACACAATCCCg                                 >  2:117290/1‑111 (MQ=255)

                                                                                                                  cGATTGCCAATGCCAGTCAGGCGGCGTGAACCCATTCAAACTGCGCCATGGTTCACCTCCAGTTCAGGTTTACGCGCTTTACGGGTACCTGATTTTATCAACACAATCCCg                                 <  1:117290/111‑1 (MQ=255)

                                                                                                                     ttGCCAATGCCAGTCAGGCGGCGTGAACCCATTCAAACTGCGCCATGGTTCACCTcc                                                                                    <  2:596600/57‑1 (MQ=255)

                                                                                                                     ttGCCAATGCCAGTCAGGCGGCGTGAACCCATTCAAACTGCGCCATGGTTCACCTcc                                                                                    >  1:596600/1‑57 (MQ=255)

                                                                                                                     ttGCCAATGCCAGTCAGGCGGCGTGAACCCATTCAAACTGCGCCATGGTTCACCTCCAGTTCAGGTTTACGCGCTTTACGGGTACCTGATTTTATCAACACAATCCCGGCGACCAGGGTGGTTAACCCGGCAATTTtca  >  1:1529321/1‑139 (MQ=255)

CTTGAGAAAGCGCACTAAAGGCAGCCAGCACCGCCGCCAGGGAGAGCAAGCCAAATATTTTGCGACGAAAGCCGTCAGAAAATTTCAAAAAGACGTTAGCAACGATTTCCAGCACGATTGCCAATGCCAGCCAGGCGGCGTGAACCCATTCAAACTGCGCCATGGTTCACCTCCAGTTCAGGTTTACGCGCTTTACGGGTACCTGATTTTATCAACACAATCCCGGCGACCAGGGTGGTTAACCCGGCAATTTTCA  >  NC_000913/1672987‑1673242

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A