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
A3 F108 I1 R1	17	38.6	1469306	86.0%	1263603	142.5

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,132,787	A→C	I204S (ATC→AGC)	wcaA ←	putative glycosyl transferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,132,787	0	A	C	97.1%	86.3 / NA	34	I204S (ATC→AGC)	wcaA	putative glycosyl transferase
Reads supporting (aligned to +/- strand): ref base A (1/0); new base C (15/18); total (16/18)
Fisher's exact test for biased strand distribution p-value = 4.71e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.56e-01

TAGAGGGTAAACAGCTGATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGAAGATGTCGTAATCCTGTGCCGCTTTCAGTTCGGTATCGAACAAACACTCTTTGAAACGCCATGCCCAGGTAAAGACCT  >  NC_000913/2132655‑2132922

tAGCGGGTAAACAGCTGATATTGTGTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGTAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGc                                                                                                                               <  2:294926/143‑1 (MQ=255)

tAGAGGGTAAACAGCTGATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGCGATCTGCACTTCATCCAGCCTGACATGCAGCCTCTGCGACGc                                                                                                                               >  2:603717/1‑143 (MQ=255)

            aGCTGATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGCTTGATGTGCAGGCTCTGCGTCGCCTCTTCTACttt                                                                                                                   >  1:506801/1‑143 (MQ=255)

            aGCTGATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGAAAGAACTGCGTCGCCACTTATACttg                                                                                                                   >  1:422252/1‑142 (MQ=255)

                 atatTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATACGCCGGCTCTGCGTCGCCTCGTCTCCTTTCCACg                                                                                                              >  1:634554/1‑143 (MQ=255)

                      ttttGCTGGCGTGGTTGTATTTGTCTTTGTGCTTGTGGTAAAAGTGGAAGTACCCGGAGAAGGTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCg                                                                                                         <  1:345141/143‑1 (MQ=255)

                       tttGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGACAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTACGTGGCCTCTTCTACTATCGACggaccga                                                                                                        >  2:393374/1‑138 (MQ=255)

                            tGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTAc                                                                                                   <  1:260008/143‑1 (MQ=255)

                              gcgcTGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTTATCTGCATTTCACCGTGATTGATATGCAGGCTCTGTGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTc                                                                                                 <  1:582421/143‑1 (MQ=255)

                                   gTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTAc                                                                                                   <  2:612339/136‑1 (MQ=255)

                                   gTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTAc                                                                                                   >  1:612339/1‑136 (MQ=255)

                                            ttCTTTGTGCTTGCGGTAGAAGCGGAAGTACCCGGAGGAGCTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCa                                                                                   <  1:43355/142‑1 (MQ=255)

                                               tttGTGCTTGCGGTAAAAGTGGAAGTACCCGTAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGa                                                                                >  2:263991/1‑143 (MQ=255)

                                                  gtgCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCACGGTCCTCTCCCACCATCCGCCggcaca                                                                             >  2:111962/1‑139 (MQ=255)

                                                      ttGCGGTAAAATTGTAAGTACTCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGAAGATGTc                                                                         <  1:503417/143‑1 (MQ=255)

                                                      ttGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGAAGATGTc                                                                         >  1:248305/1‑143 (MQ=255)

                                                      ttGCGGAAAAAGAAGAAGGAACCGGAAAATAGTTTCGGAGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGAAGATGTc                                                                         <  1:157798/143‑1 (MQ=255)

                                                        gCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCCTTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACAATCCGCAGGAAGCTGTCGt                                                                       >  1:545392/1‑143 (MQ=255)

                                                           gTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTCCTCCACCACCCTCCGCACGACGATGTCGGAAt                                                                    >  1:732121/1‑143 (MQ=255)

                                                                aGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTGCTCCACCACCATCCGCAGGCAGATGAAGTAACCCcgt                                                               >  2:650640/1‑143 (MQ=255)

                                                                aGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGAAGATGTCGTAATCCtgt                                                               >  1:310175/1‑143 (MQ=255)

                                                                    taaGTACCCGGAGAGTTTTTTCGGTGACTAGGTGATCTTCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTGCACGGTTCGCCGTACTCCACCACCATCCGCAGGAAGATGTCGTAATCCTGTGCCg                                                           <  2:670228/142‑1 (MQ=255)

                                                                      cgttcccGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCGTCTACTTTCCACGGTTCGCCGTACTCCACCACCTTCCGCAGGAAGATGTCGTAATCCTGTGCCGCt                                                         <  2:491273/139‑1 (MQ=255)

                                                                                    tttttCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGAAGATGTCGTAATCCTGTGCCGCTTTCAGTTCGGTATc                                           <  2:603678/143‑1 (MQ=255)

                                                                                     ttttCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCGCGGTTCGCCGTACTCCACCACCATCCGCAGGAAGATGTCGTAATCCTGTGCCGCTTTCAGTTCGGTATCg                                          <  2:310175/143‑1 (MQ=255)

                                                                                     ttttCGGAGACGAAGTGATCTGCATCTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGAAGATGTCGTAATCCTGTGCCGCTTTCAGTTCGGTATCg                                          <  1:442070/143‑1 (MQ=255)

                                                                                                  ggTGATCTGCATTTCACCGTGATTGATATGCAGGCTCTCCGTCGCCTCTTCTTCTGTCGACGGTTCGCCGTACTCCACCGCCATCCCCTGGAAGATGTCGTATTCCTTTGCCGCTTTCAGTTCGGTATCGAACAAACACTCtt                             <  2:346220/143‑1 (MQ=255)

                                                                                                        cTGCATTTCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCCCCATCCGCAGCAAGATGTCGTAATCCTCTGCCGCGTTTGGTTCGGTATCGAGCAAGCACTCGTTGagca                       >  2:146130/1‑140 (MQ=255)

                                                                                                         tGCATTTCACCGTGATTGAGATGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGAAGATGTCGTAATCCTGTGCCGCTTTCAGTTCGGTATCGAACAAACACTCTTTGAAACg                      <  2:288206/143‑1 (MQ=255)

                                                                                                             tttCACCGTGATTGATATGCAGGCTCTGCGTCGCCTCTTCTCCTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGAAGATGTCGTAATCCTGTGCCGCTCTCAGTGCGGCATCGAACCAACACTCCTTGAGACGCCAt                  >  2:118856/1‑143 (MQ=255)

                                                                                                                   cGTGATTGATTTGCATGCTTCGCGTCTCCTCTTCTACTTTCCACGGTTCGTCGTGCTCCACCACGATCCGCACGAAGATTCCGTAATCCTGTGCCGCTTTCAGTTCGGTATCGAACAAACACTCTTTGAAACGCCATGCCCAg            <  2:308173/143‑1 (MQ=255)

                                                                                                                        ttgacATGCAGGCTCTTCGTCTCTTCTTATACTGTCCACGTTTCGCCTTACTCCACCACTATCCTCATGAAGATTTCGTAATCCTGTGCCGCTGTCAGTTCGGTATTGAACAAACACTTTTTGAAACGCCATGCCCAGGTaaa       <  2:731206/143‑1 (MQ=255)

                                                                                                                           atatGCAGGCTCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGCCTATGTCGTAATCCTGTGCCGCTTTCAGTTCGGTAACGAACAAACACTCTTTGAAACGCCATGCCCAGGTAAAGAc    >  1:225431/1‑143 (MQ=255)

                                                                                                                             attcAGGCTTTGCGTCGCCTCTTCTCCTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGAAGATGTCGTAATCCTGTGCCGCTTTCAGTTCGGTATCGAACAAACACTCTTTGAAACGCCATGCCCAGGTAAAGACCt  <  2:248305/140‑1 (MQ=255)

TAGAGGGTAAACAGCTGATATTTTTTGCTGGCGCGGTCGAATTTGTCTTTGTGCTTGCGGTAAAAGTGGAAGTACCCGGAGAATTTTTTCGGTGACGAGGTGATCTGCATTTCACCGTGATTGATATGCAGGATCTGCGTCGCCTCTTCTACTTTCCACGGTTCGCCGTACTCCACCACCATCCGCAGGAAGATGTCGTAATCCTGTGCCGCTTTCAGTTCGGTATCGAACAAACACTCTTTGAAACGCCATGCCCAGGTAAAGACCT  >  NC_000913/2132655‑2132922

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 8 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A