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 F13 I0 R1	90	33.2	766976	92.9%	712520	140.9

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%	114.4 / NA	36	intergenic (‑96/‑20)	nanA/nagC	N‑acetylneuraminate lyase/possible transcriptional regulator
Reads supporting (aligned to +/- strand): ref base G (0/0); new base T (21/15); total (21/15)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TTAAATCTTTGTTCATTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTAGTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTAAATCGGCAGTTATTGATAAGCAATTGAATAT  >  CP000730/367533‑367776

ttAAATCTTTGTTCATTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGt                                                                                                         <  2:84627/141‑1 (MQ=255)

ttAAATCTTTGTTCATTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGt                                                                                                         >  1:338213/1‑141 (MQ=255)

 tAAATCTTTGTTCATTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATAATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATAAAAATGtt                                                                                                        >  2:243408/1‑141 (MQ=255)

   aaTCTTTGTTCATTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTACTGAAAATGtttt                                                                                                      >  2:83557/1‑141 (MQ=255)

   aaTCTTTGTTCATTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGtttt                                                                                                      >  1:118627/1‑141 (MQ=255)

   aaTCTTTGTTCATTATGAAGTCCCTCCAAAAATCATTAGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGtttt                                                                                                      >  2:251514/1‑141 (MQ=255)

             cATTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCaa                                                                                            <  2:101306/141‑1 (MQ=255)

                    aaGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTTTTTTTTTTTTTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAAGCAATAGAAAt                                                                                     >  2:192759/1‑141 (MQ=255)

                    aaGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAAt                                                                                     >  1:363904/1‑141 (MQ=255)

                    aaGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAAt                                                                                     >  1:39423/1‑141 (MQ=255)

                               aaaaTCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTaa                                                                          >  1:291922/1‑141 (MQ=255)

                                   tCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAACATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAggag                                                                      >  2:246171/1‑139 (MQ=255)

                                   tCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGgtg                                                                      <  1:71797/141‑1 (MQ=255)

                                         gATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTAc                                                                <  2:227901/141‑1 (MQ=255)

                                              tataGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTTAGGTGTATTACATCGc                                                           <  1:226780/141‑1 (MQ=255)

                                                         gCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTTTTTTTTTTTTTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATATAAATGGAGTGAGTCAGGTGTATTACATCGCAATCGATATTg                                                >  2:164756/1‑141 (MQ=255)

                                                           tataATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATAGATATTGGa                                              >  2:32555/1‑141 (MQ=255)

                                                            ataATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAAGGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAg                                             >  1:164536/1‑141 (MQ=255)

                                                                ttGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCAc                                         >  2:17896/1‑141 (MQ=255)

                                                                   tAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTTTGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCa                                      <  2:263377/141‑1 (MQ=255)

                                                                     aaggCTATCATAAAATGTAACAATATCTTTTGGAAAATTGTATTCATATTTATGTATAATTAAGGAAAATGTTTTTCAAAATCAATAGAAATGAAGTGAGTAAGGTGTATTATATAGCAATCGATATTGGTGGCACTCaaa                                    <  2:185050/138‑1 (MQ=255)

                                                                     aaCGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCaaa                                    >  2:272679/1‑141 (MQ=255)

                                                                      aCGCTATCATAAAATGTAACAATATCTTTTTTTTTTTTTTTTTTATATTTATGTATAATTAATGAAAATTTTTTTCAAAATCATTAGAAATGGAGTGAGTAAGGTGTATTACTTCGTAATCGTTAtttcaggtatgcaaaa                                   >  2:248682/1‑127 (MQ=255)

                                                                        gCTATCATAAAATGTAACAATATCATTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTa                                 <  1:125063/141‑1 (MQ=255)

                                                                        gCTATAATAAAATGTAAAAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTa                                 <  1:34180/141‑1 (MQ=255)

                                                                                aaaaTGGAACAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTAAATCGGCa                         <  1:107195/141‑1 (MQ=255)

                                                                                       aaCAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTAAATCGGCAGTTATTg                  <  2:39423/141‑1 (MQ=255)

                                                                                        aCAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTAAATCGGCAGTTATTGa                 >  1:324781/1‑141 (MQ=255)

                                                                                        aCAATATCTTTTTGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTAAATCGGCAGTTATTGa                 >  1:290402/1‑141 (MQ=255)

                                                                                          aaTATCTTTTTGAAACTTGTATTCAAATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTGAATCGGCAGTTATTGATa               >  1:191681/1‑141 (MQ=255)

                                                                                                tttttGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTAAATCGGCAGTAATTGATAAGAAAt         >  1:175221/1‑141 (MQ=255)

                                                                                                 ttttGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTAAATCGGCAGTTATTGATAAGCAAtt        <  2:378332/141‑1 (MQ=255)

                                                                                                    tGAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTAAATCGGCAGGTATTGATAAGCAATTGaa     <  1:361700/141‑1 (MQ=255)

                                                                                                     gAAAATTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTAAATCGGAAGATATTGATACGCAAttacgt    >  1:27446/1‑137 (MQ=255)

                                                                                                       aaaTTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTAAATCGGCAGTTATTGATAAGCAATTGAatat  <  1:251514/141‑1 (MQ=255)

                                                                                                       aaaTTGTATTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTAAATCGGCAGTTATTGATAAGCAATTGAatat  <  1:83557/141‑1 (MQ=255)

TTAAATCTTTGTTCATTATGAAGTCCCTCCAAAAATCATTTGATAATATAGTTTACAGCTATAATTGTAAACGCTATCATAAAATGTAACAATATCTTTTTGAAAATTGTAGTCATATTTATGTATAATTAATGAAAATGTTTTTCAAAATCAATAGAAATGGAGTGAGTAAGGTGTATTACATCGCAATCGATATTGGAGGCACTCAAATTAAATCGGCAGTTATTGATAAGCAATTGAATAT  >  CP000730/367533‑367776

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A