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
A2 F1 I2 R1	764	42.0	2018750	95.5%	1927906	109.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,563,520	G→T	intergenic (+403/‑72)	yffP → / → yffQ	CPZ‑55 prophage, uncharacterized protein/CPZ‑55 prophage, uncharacterized protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,563,520	0	G	T	100.0%	114.2 / NA	36	intergenic (+403/‑72)	yffP/yffQ	CPZ‑55 prophage, uncharacterized protein/CPZ‑55 prophage, uncharacterized protein
Reads supporting (aligned to +/- strand): ref base G (0/0); new base T (16/20); total (16/20)

TCAACTCCCACCAAAGCCAACAAGATGGGAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCAATCATCCTGATGGTGCTGACTGGTGTTTGCTTTGCAGATGTTG  >  NC_000913/2563385‑2563652

tCAACTCCCACCAAAGCCAACAAGATGGGAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTACCCAACAACAAAATAAAGATGGGAGGTAAAAATTaaa                                                                                                                                   <  2:119343/139‑1 (MQ=255)

    cTCCCACCAAAGCCAACAAGATGGGAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGt                                                                                                                               >  1:878635/1‑139 (MQ=255)

         accaAAGCCAACAAGATGGGAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGTGGGaa                                                                                                                          >  1:698962/1‑139 (MQ=255)

           caAAGCCAACAAGATGGGAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGt                                                                                                                        <  2:258359/139‑1 (MQ=255)

            aaaGCCAACAAGATGGGAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGTGGGaa                                                                                                                          <  2:927736/136‑1 (MQ=255)

            aaaGCCAACAAGATGGGAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGTGGGaa                                                                                                                          >  1:927736/1‑136 (MQ=255)

             aaGCCAACAAGATGGGAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTgg                                                                                                                      <  1:234758/139‑1 (MQ=255)

                       gATGGGAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGt                                                                                                            <  2:878635/139‑1 (MQ=255)

                       gATGGGAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGt                                                                                                            <  2:27926/139‑1 (MQ=255)

                          gggAGGAGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGT‑GCTTTACTGGTGATg                                                                                                        >  1:894438/1‑139 (MQ=255)

                               gTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTaa                                                                                                    >  1:357865/1‑139 (MQ=255)

                                 gAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATg                                                                                                  <  2:698962/139‑1 (MQ=255)

                                         tgATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTg                                                                                          <  1:323414/139‑1 (MQ=255)

                                           aTGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCt                                                                                        <  2:357865/139‑1 (MQ=255)

                                                   cGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGaa                                                                                <  1:825363/139‑1 (MQ=255)

                                                   cGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGaa                                                                                <  2:559050/139‑1 (MQ=255)

                                                                cAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTaaa                                                                                                                                   >  2:224921/1‑75 (MQ=255)

                                                                cAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTaaa                                                                                                                                   <  1:224921/75‑1 (MQ=255)

                                                                  ggCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATg                                                                                                        >  1:313135/1‑100 (MQ=255)

                                                                  ggCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATg                                                                                                        <  2:313135/100‑1 (MQ=255)

                                                                                 ttCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTa                                                                                                                 >  1:54193/1‑76 (MQ=255)

                                                                                 ttCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTa                                                                                                                 <  2:54193/76‑1 (MQ=255)

                                                                                      tcaaCGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCa                                             <  2:806530/139‑1 (MQ=255)

                                                                                              aGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGt                                                                                                            <  1:636883/68‑1 (MQ=255)

                                                                                              aGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGt                                                                                                            >  2:636883/1‑68 (MQ=255)

                                                                                                    ttCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCaa                                            <  1:108632/126‑1 (MQ=255)

                                                                                                    ttCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCaa                                            >  2:108632/1‑126 (MQ=255)

                                                                                                    ttCCCAACAACAAAATAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCAATCATCCTGATGGt                               >  1:415839/1‑139 (MQ=255)

                                                                                                                 aaTAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACtg                                                                             <  2:450789/80‑1 (MQ=255)

                                                                                                                 aaTAAAGATGGGAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACtg                                                                             >  1:450789/1‑80 (MQ=255)

                                                                                                                           ggAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGaa                                                                                <  2:499247/67‑1 (MQ=255)

                                                                                                                           ggAGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGaa                                                                                >  1:499247/1‑67 (MQ=255)

                                                                                                                             aGGTAAAAATTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCAATCATCCTGATGGTGCTGACTGGTGTTTGCTTTGCAGAt      >  2:13523/1‑139 (MQ=255)

                                                                                                                                 aaaaaTTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCAATCATCCTGATGGTGCTGACTGGTGTTTGCTTTGCAGATGTTg  >  2:33039/1‑139 (MQ=255)

                                                                                                                                  aaaaTTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTa                                                                                     >  2:323963/1‑55 (MQ=255)

                                                                                                                                  aaaaTTAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTa                                                                                     <  1:323963/55‑1 (MQ=255)

TCAACTCCCACCAAAGCCAACAAGATGGGAGGTGAATTTTGTGATGCAGATCGCTTTTTCCCTTCAGGCATTTTTGTTTAATTCAATCAACGAAAGGCAGTTCCCAACAACAAAATAAAGATGGGAGGTAAAAATGAAACGGTGGGAAGTGGCTTTACTGGTGATGGTAATGTTGGTTTGCTGTATTGAACTGTGAAGGAGGACGCCATGAAACTTTTAATCGCAATCATCCTGATGGTGCTGACTGGTGTTTGCTTTGCAGATGTTG  >  NC_000913/2563385‑2563652

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A