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
A17 F172 I0 R1	42	33.2	716278	96.8%	693357	139.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	367,644	G→T	100%	intergenic (‑96/‑20)	nanA ← / → nagC	N‑acetylneuraminate lyase/possible transcriptional regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	367,644	0	G	T	100.0%	88.4 / ‑6.5	30	intergenic (‑96/‑20)	nanA/nagC	N‑acetylneuraminate lyase/possible transcriptional regulator
Reads supporting (aligned to +/- strand): ref base G (0/0); major base T (17/12); minor base C (0/1); total (17/13)
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

ACGAGTAACGCTGCATATAAACCTTTTAAATCTTTGTTCATTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTAGTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTAAATCGGCAGTTATTGATAAGCAATTGAATAT  >  CP000730/367508‑367776

aCGAGTAACGCTGCATATAAACCTTTTAAATCTATGTTCATTATGAAGTCACTCCGAAAATCATTTGATAATATAGTTTACAACTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCa                                                                                                                                   >  2:235077/1‑140 (MQ=255)

   aGTAACGCTGCATATAAACCTTTTAAATCTTTGTTCATTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCatat                                                                                                                                >  2:144228/1‑140 (MQ=255)

       aCGCTTCATATAATCGTTTTAAATCTTTGTTCATTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTAt                                                                                                                            <  1:6271/140‑1 (MQ=255)

        cGCTGCATATAAACCTTTTAAATCTTTGTTCATTATGAAGTCCCTCCATAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATg                                                                                                                           <  1:275874/140‑1 (MQ=255)

          cTGCATATAAACCTTTTAAATCTTTGTTCATTATGAAGTCCCTCAAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTGTTTGAAAATAGTATTCATATTTTTGta                                                                                                                         >  1:201258/1‑140 (MQ=255)

                          tAAATCTTTGTTCATTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTTTATTCATCTTTATGTATAATTAATGAAAATGt                                                                                                         >  2:13004/1‑140 (MQ=255)

                            aaTCTTTGTTCATTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATGATAAAATGTAACAATATCTTTTTAGAAGTTATATTCATATTTATGTATAATTTATGAAAATGttt                                                                                                       >  2:107810/1‑140 (MQ=255)

                            aaTCTTTGTTCATTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGttt                                                                                                       >  2:269535/1‑140 (MQ=255)

                                        ttATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAAt                                                                                           <  1:126758/140‑1 (MQ=255)

                                        atATGAAGGCCCTCAAAAAATCATTTTATTATATAGTATAAAGCTATATTTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAAt                                                                                           <  2:127861/139‑1 (MQ=255)

                                              aGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAAt                                                                                     <  2:241162/140‑1 (MQ=255)

                                                    tCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGgagtg                                                                               <  1:269535/140‑1 (MQ=255)

                                                         aaaTCATTTGATAATATAGTTTACAGCTATAATTGTAGACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTaa                                                                          >  2:193667/1‑140 (MQ=255)

                                                             cATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGAATAATTAATAAAAATGTTTTTAAAAATCAATAGAAATGGAGTGAGTAAggag                                                                      >  1:6465/1‑138 (MQ=255)

                                                                ttGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCACTAGAAATGGAGTGAGTAAGGTGTAt                                                                   >  1:91380/1‑140 (MQ=255)

                                                                                          tGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTAAATCGTAATCGTTATTGGAGGTAc                                         >  1:307514/1‑140 (MQ=255)

                                                                                          tGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTCATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCAc                                         >  1:237493/1‑140 (MQ=255)

                                                                                            tAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTc                                       <  2:118299/140‑1 (MQ=255)

                                                                                             aaaCGCTATCATAAAATGTAACAATATCTTTTTTAAATTTTTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGCAGACACTCa                                      >  2:33938/1‑140 (MQ=255)

                                                                                               aCGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATGAATATAAATGGAGTGAGTAAGGGGTATTACATCGCAATAGATATTGGAGGCAcactaa                                    >  1:82976/1‑135 (MQ=255)

                                                                                                cGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAAt                                   <  1:144324/140‑1 (MQ=255)

                                                                                                     tCATAAAATGTAACAATATCTTTTTGAAAATGGTATTCATCTTTCTGTATAATTCATGAAAATGTTTTTCAAAATCAATAGAAATGAAGTGAGTAAGGTGTATTACATCGCAATCGATATTGAAGACACTCAAATTAAAt                              >  1:69246/1‑140 (MQ=255)

                                                                                                       aTAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAAAAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGAAGGCACTCAAATTAAATCg                            >  1:34203/1‑140 (MQ=255)

                                                                                                          aaaTGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTAAATCggaa                         >  1:91015/1‑138 (MQ=255)

                                                                                                            aTGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCATAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTAAATCGGCAGt                       <  2:305118/140‑1 (MQ=255)

                                                                                                              taaataaTATCTTTTTGAAAATTATATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTAAATCGGCAGTTa                     <  1:107810/135‑1 (MQ=255)

                                                                                                                   aaTATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTAAATCGGCAGTTATTGAt                <  1:144228/140‑1 (MQ=255)

                                                                                                                            tttaaaaTTGTACTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCTCAATCGATATTGGAGGCCCTCAAATTAAATCGGCAGTTATTGATAAGCAATTg       <  2:185652/137‑1 (MQ=255)

                                                                                                                              gAAATTTTTATTTATATTTATTTATAATTAATGAAAATGTTTTTCACAATCCATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTAAATCGGCAGTTATTGATAAGCAATTGaa     <  2:201183/140‑1 (MQ=255)

                                                                                                                                 aaTTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTAAATCGGCAGTTATTGCTAAGCAATTGAatat  >  2:171678/1‑140 (MQ=255)

ACGAGTAACGCTGCATATAAACCTTTTAAATCTTTGTTCATTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTAGTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTAAATCGGCAGTTATTGATAAGCAATTGAATAT  >  CP000730/367508‑367776

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