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
A6 F1 I1 R1	750	51.0	2595496	93.6%	2429384	106.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,742,599	Δ1 bp	intergenic (‑67/‑134)	yiaJ ← / → yiaK	transcriptional repressor for the yiaKLMNO‑lyxK‑sgbHUE operon/2,3‑diketo‑L‑gulonate reductase, NADH‑dependent

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,742,599	0	C	.	81.6%	125.8 / 33.8	49	intergenic (‑67/‑134)	yiaJ/yiaK	transcriptional repressor for the yiaKLMNO‑lyxK‑sgbHUE operon/2,3‑diketo‑L‑gulonate reductase, NADH‑dependent
Reads supporting (aligned to +/- strand): ref base C (5/4); new base . (22/18); total (27/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.75e-01

CGCCATCTCGTTCTCTTTTTTTCCCATCACTTCTTTCCCCATTTTGTCGCGTCCTGATGGTAGCGCAAAGTGTGCCGTAGTTCACGATCTCGACAGATAATTTATAACCAATTGATTTTTATGTCTTTTGAAATTCATCAATCAGATTGCCTTGTTAAAAAGTGATCGATATAT  >  NC_000913/3742491‑3742664

cgcCATCTCGTTCTCTTTTTTTCCCATCACTTCTTTCCCCATTTTGTCGCGTCCTGATGGTAGCGCAAAGTGTGCCGTAGTTCACGATCTCGACAGATAATTTATAA‑CAATTGATTTTTATGTCTTTTGAAATtcatca                                    <  2:661205/139‑1 (MQ=255)

 gcCATCTCGTTCTCTTTTTTTCCCATCACTTCTTTCCCCATTTTGTCGCGTCCTGATGGTAGCGCAATGTGTGCCGTAGTTCACGATCTCGACAGATAATTTATAA‑CAATTGATTTTTATGTCTTTTGAAATTCatcaa                                   >  1:808250/1‑139 (MQ=255)

 gcCATCTCGTTCTCTTTTTTTCCCATCACTTCTTTCCCCATTTTGTCGCGTCCTGATGGTAGCGCAAAGTGTGCCGTAGTTCACGATCTCGACAGATAATTTATAA‑CAATTGATTTTTATGTCTTTTGAAATTCatcaa                                   >  2:245381/1‑139 (MQ=255)

     tctcGTTCTCTTTTTTTCCCATCACTTCTTTCCCCATTTTGTCGCGTCCTGATGGTAGCGCAAAGTGTGCCGTAGTTCACGATCTCGACAGATAATTTATAAC‑AATTGATTTTTATGTCTTTTGAAATTCATCAATCct                               <  1:17218‑M2/139‑3 (MQ=255)

        cGTTCTCTTTTTTTCCCATCACTTCTTTCCCCATTTTGTCGCGTCCTGATGGTAGCGCAAAGTGTGCCGTAGTTCACGATCTCGACAGATAATTTATAAC‑AATTGATTTTTATGTCTTTTGAAATTCATCAATCctgtt                            >  1:1291556‑M2/1‑134 (MQ=255)

          ttCTCTTTTTTTCCCATCACCTCTTTCCCCATTTTGTCGCGTCCTGATGGTAGCGCAAAGTGTGCCGTAGTTCACGATCTCGACAGATAATTTATAAC‑AATTGATTTTTATGTCTTTTGAAATTCATCAATCctgttga                          <  1:96253‑M2/139‑8 (MQ=255)

               tttttttCCCATCCCTTCTTTCCCCATTTTGTCGCGTCCTGATGGTAGCGCAAAGTGTGCCGTAGTTCACGATCTCGACAGATAATTTATAAC‑AATTGATTTTTATGTCTTTTGAAATTCATCAATCctgttgacaatt                     <  2:868879‑M2/139‑13 (MQ=255)

               tttttttCCCATCACTTCTTTCCCCATTTTGTCGCGTCCTGATGGTAGCGCAAAGTGTGCCGTAGTTCACGATCTCGACAGATAATTTATAAC‑AATTGATTTTTATGTCTTTTGAAATTCATCAATCctgttgacaatt                     <  2:533166‑M2/139‑13 (MQ=255)

                   tttCCCATCACTTCTTTCCCCATTTTGTCGCGTCCTGATGGTAGCGCAAAGTGTGCCGTAGTTCACGATCTCGACAGATAATTTATAAC‑AATTGACTTTTATGTCTTTTGAAATTCATCAATCctgttgacaattaatc                 >  2:943221‑M2/1‑123 (MQ=255)

                     tCCCATCACTTCTTTCCCCATTTTGTCGCGTCCTGATGGTAGCGCAAAGTGTGCCGTAGTTCACGATCTCGACAGATAATTTATAAC‑AATTGATTTTTATGTCTTTTGAAATTCATCAATCctgttgacaattaatcat               >  1:307241‑M2/1‑121 (MQ=255)

                       ccATCACTTCTTTCCCCATTTTGTCGCGTCCTGATGGTAGCGCAAAGTGTGCCGTAGTTCACGATCTCGACAGATAATTTATAAC‑AATTGATTTTTATGTCTTTTGAAATTCATCAATCctgttgacaattaatcatcg             >  2:17218‑M2/1‑119 (MQ=255)

                        cATCACTTCTTTCCCCATTTTGTCGCGTCCTGATGGTAGCGCAAAGTGTGCCGTAGTTCACGATCTCGACAGATAATTTATAAC‑AATTGATTTTTATGTCTTTTGAAATTCATCAATCctgttgacaattaatcatcga            >  2:808250‑M2/1‑118 (MQ=255)

                         aTCACTTCTTTCCCCATTTTGTCGCGTCCTGATGGTAGCGCAAAGTGTGCCGTAGTTCACGATCTCGACAGATAATTTATAAC‑AATTGATTTTTATGTCTTTTGAAATTCATCAATCctgttgacaattaatcat               <  2:806028‑M2/135‑19 (MQ=255)

                         aTCACTTCTTTCCCCATTTTGTCGCGTCCTGATGGTAGCGCAAAGTGTGCCGTAGTTCACGATCTCGACAGATAATTTATAAC‑AATTGATTTTTATGTCTTTTGAAATTCATCAATCctgttgacaattaatcat               >  1:806028‑M2/1‑117 (MQ=255)

                          tCACTTCTTTCCCCATTTTGTCGCGTCCTGATGGTAGCGCAAAGTGTGCCGTAGTTCACGATCTCGACAGATAATTTATAAC‑AATTGATTTTTATGTCTTTTGAAATTCATCAATCctgttgacaattaatcatcggca          >  2:993240‑M2/1‑116 (MQ=255)

                           cACTTCTTTCCCCATTTTGTCGCGTCCTGATGGTAGCGCAAAGTGTGCCGTAGTTCACGATCTCGACAGATAATTTATAAC‑AATTGATTTTTATGTCTTTTGAAATTCATCAATCctgttgacaattaagcatcggcat         >  1:868879‑M2/1‑115 (MQ=255)

                              ttcttTCCCCATTTTGTCGCGTCCTGATGGTAGCGCAAAGTGTGCCGTAGTTCACGATCTCGACAGATAATTTATAAC‑AATTGATTTTTATGTCTTTTGAAATTCATCAATCctgttgacaattaatcatcggcatag       <  1:1108351‑M2/138‑27 (MQ=255)

                              ttcttTCCCCATTTTGTCGCGTCCTGATGGTAGCGCAAAGTGTGCCGTAGTTCACGATCTCGACAGATAATTTATAAC‑AATTGATTTTTATGTCTTTTGAAATTCATCAATCctgttgacaattaatcatcggcatag       >  2:1108351‑M2/1‑112 (MQ=255)

                                cttTCCCCATTTTGTCGCGTCCTGATGGTAGCGCAAAGTGTGCCGTAGTTCACGATCTCGACAGATAATTTATAAA‑AATTGATTTTTATGTCTTTTGAAATTCATCAATCctgtt                            <  1:998513‑M2/115‑6 (MQ=255)

                                cttTCCCCATTTTGTCGCGTCCTGATGGTAGCGCAAAGTGTGCCGTAGTTCACCATCTCGACAGATAATTTATAAC‑AATTGATTTTTATGTCTTTTGAAATTCATCAATCctgtt                            >  2:998513‑M2/1‑110 (MQ=255)

                                  ttCCCCATTTTGTCGCGTCCTGATGGTAGCGCAAAGTGTGCCGTAGTTCACGATCTCGACAGATAATTTATAAC‑AATTGATTTTTATGTCTTTTGAAATTCATCAATCctgttgacaattaatcatcggcatagtatat  >  1:245381‑M2/1‑108 (MQ=255)

                                        aTTTTGTCGCGTCCTGATGGTAGCGCAAAGTGTGCCGTAGTTCACGATCTCGACAGATAATTTATAAC‑AATTGATTTTTATGTCTTTTGAAATTCATCAATCctgttgacaattaatc                 >  2:1035381‑M2/1‑102 (MQ=255)

                                        aTTTTGTCGCGTCCTGATGGTAGCGCAAAGTGTGCCGTAGTTCACGATCTCGACAGATAATTTATAAC‑AATTGATTTTTATGTCTTTTGAAATTCATCAATCctgttgacaattaatc                 <  1:1035381‑M2/118‑17 (MQ=255)

                                               cgcgTCCTGATGGTAGCGCAAAGTGTGCCGTAGTTCACGATCTCGACAGATAATTTATAA‑CAATTGATTTTTATg                                                     <  1:650001/75‑1 (MQ=255)

                                               cgcgTCCTGATGGTAGCGCAAAGTGTGCCGTAGTTCACGATCTCGACAGATAATTTATAA‑CAATTGATTTTTATg                                                     >  2:650001/1‑75 (MQ=255)

                                                   tCCTGATGGTAGCGCAAAGTGTGCCGTAGTTCACGATCTCGACAGATAATTTATAAC‑AATTGATTTTTATGTCTTTTGAAATTCATCAATCctgttgacaattaatcat               <  2:894814‑M2/109‑19 (MQ=255)

                                                   tCCTGATGGTAGCGCAAAGTGTGCCGTAGTTCACGATCTCGACAGATAATTTATAAC‑AATTGATTTTTATGTCTTTTGAAATTCATCAATCctgttgacaattaatcat               >  1:894814‑M2/1‑91 (MQ=255)

                                                   tCCTGATGGTAGCGCAAAGTGTGCCGTAGTTCACGATCTCGACAGATAATTTATAAC‑AATTGATTTTTATGTCTTTTGAAATTCATCAATCctgttgacaattaat                  >  1:49880‑M2/1‑91 (MQ=255)

                                                   tCCTGATGGTAGCGCAAAGTGTGCCGTAGTTCACGATCTCGACAGATAATTTATAAC‑AATTGATTTTTATGTCTTTTGAAATTCATCAATCctgttgacaattaat                  <  2:49880‑M2/106‑16 (MQ=255)

                                                            tAGCGCAAAGTGTGCCGTAGTTCACGATCTCGACAGATAATTTATAAC‑AATTGATTTTTATGTCTTTTGAAATTCATCAATCctgttgacaattaatcatcggcat         <  1:327969‑M2/106‑25 (MQ=255)

                                                            tAGCGCAAAGTGTGCCGTAGTTCACGATCTCGACAGATAATTTATAAC‑AATTGATTTTTATGTCTTTTGAAATTCATCAATCctgttgacaattaatcatcggcat         >  2:327969‑M2/1‑82 (MQ=255)

                                                              gcgcAAAGTGTGCCGTAGTTCACGATCTCGACAGATAATTTATAAC‑AATTGATTTTTATGTCTTTTGAAATTCATCAATCctgttgacaattaatcatcggcatagtata   >  1:89773‑M2/1‑80 (MQ=255)

                                                              gcgcAAAGTGTGCCGTAGTTCACGATCTCGACAGATAATTTATAAC‑AATTGATTTTTATGTCTTTTGAAATTCATCAATCctgttgacaattaatcatcggcatagtata   <  2:89773‑M2/110‑31 (MQ=255)

                                                              gcgcAAAGTGTGCCGTAGTTCACGATCTCGACAGATAATTTATAAC‑AATTGATTTTTATGTCTTTTGAAATTCATCAATCctgttgacaattaatcatcggcat         >  1:1094035‑M2/1‑80 (MQ=255)

                                                              gcgcAAAGTGTGCCGTAGTTCACGATCTCGACAGATAATTTATAAC‑AATTGATTTTTATGTCTTTTGAAATTCATCAATCctgttgacaattaatcatcggcat         <  2:1094035‑M2/104‑25 (MQ=255)

                                                               cgcAAAGTGTGCCGTAGTTCACGATCTCGACAGATAATTTATAAC‑AATTGATTTTTATGTCTTTTGAAATTCATCAATCctgttgacaattaatcat               <  2:605196‑M2/97‑19 (MQ=255)

                                                               cgcAAAGTGTGCCGTAGTTCACGATCTCGACAGATAATTTATAAC‑AATTGATTTTTATGTCTTTTGAAATTCATCAATCctgttgacaattaatcat               >  1:605196‑M2/1‑79 (MQ=255)

                                                                  aaaGTGTGCCGTAGTTCACGATCTCGACAGATAATTTATAA‑CAATTGATTTTTATGTCTTTTg                                              <  2:825283/63‑1 (MQ=255)

                                                                  aaaGTGTGCCGTAGTTCACGATCTCGACAGATAATTCATAA‑CAATTGATTTTTATGTCTTTTg                                              >  1:825283/1‑63 (MQ=255)

                                                                     gtgtGCCGTAGTTCACGATCTCGACAGATAATTTATAA‑CAATTGATTTTTa                                                       <  1:944114/51‑1 (MQ=255)

                                                                     gtgtGCCGTAGTTCACGATCTCGACAGATAATTTATAA‑CAATTGATTTTTa                                                       >  2:944114/1‑51 (MQ=255)

                                                                           cGTAGTTCACGATCTCGACAGATAATTTATAAC‑AATTGATTTTTATGTCTTTTGAAATTCATCAATCctgttgacaattaatcatcggcat         <  2:906673‑M2/91‑25 (MQ=255)

                                                                           cGTAGTTCACGATCTCGACAGATAATTTATAAC‑AATTGATTTTTATGTCTTTTGAAATTCATCAATCctgttgacaattaatcatcggcat         >  1:906673‑M2/1‑67 (MQ=255)

                                                                                ttCACGATCTCGACAGATAATTTATAAC‑AATTGATTTTTATGTCTTTTGAAATTCATCAATCctgtt                            <  1:156726‑M2/67‑6 (MQ=255)

                                                                                ttCACGATCTCGACAGATAATTTATAAC‑AATTGATTTTTATGTCTTTTGAAATTCATCAATCctgtt                            >  2:156726‑M2/1‑62 (MQ=255)

                                                                                                  aaTTTATAAC‑AATTGATTTTTATGTCTTTTGAAATTCATCAATCctgttgacaattaatcat               <  2:654773‑M2/62‑19 (MQ=255)

                                                                                                  aaTTTATAAC‑AATTGATTTTTATGTCTTTTGAAATTCATCAATCctgttgacaattaatcat               >  1:654773‑M2/1‑44 (MQ=255)

                                                                                                      tataAC‑AATTGATTTTTATGTCTTTTGAAATTCATCAATCctgttgacaattaatcat               <  1:1275681‑M2/58‑19 (MQ=255)

                                                                                                      tataAC‑AATTGATTTTTATGTCTTTTGAAATTCATCAATCctgttgacaattaatcat               >  2:1275681‑M2/1‑40 (MQ=255)

CGCCATCTCGTTCTCTTTTTTTCCCATCACTTCTTTCCCCATTTTGTCGCGTCCTGATGGTAGCGCAAAGTGTGCCGTAGTTCACGATCTCGACAGATAATTTATAACCAATTGATTTTTATGTCTTTTGAAATTCATCAATCAGATTGCCTTGTTAAAAAGTGATCGATATAT  >  NC_000913/3742491‑3742664

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A