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
A4 F1 I2 R1	780	68.3	3343050	93.5%	3125751	102.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,212,088	(C)_8→9	intergenic (‑85/+615)	iraM ← / ← ycgX	RpoS stabilzer during Mg starvation, anti‑RssB factor/DUF1398 family protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,212,080	1	.	C	94.1%	47.3 / ‑3.1	17	intergenic (‑77/+623)	iraM/ycgX	RpoS stabilzer during Mg starvation, anti‑RssB factor/DUF1398 family protein
Reads supporting (aligned to +/- strand): ref base . (1/0); new base C (11/5); total (12/5)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TCAATTACTATCCACTTCATTTGTTATGTCTTATCCCACGGTATTTAATATGGTTCATTAGGATGTTTATTTCTTGATTTTGCATATGAGTATATT‑A‑‑CCCCCCCCTCAAAAAAATAAATTAATTAAAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTT  >  NC_000913/1211984‑1212206

tCAATTACTATCCACTTCATTTGTTATGTCTTATCCCACGGTATTTAATATGGTTCATTAGGATGTTTATTTCTTGATTTTGCATATGAGTATATT‑AC‑CCCCCCCCTCAAAAAAATAAATTAATAAAAATATTGGCTta                                                                                       >  2:147856/1‑139 (MQ=255)

                    ttGTTATGTCTTATCCCACGGTATTTAATATGGTTCATTAGGATGTTTATTTCTTGATTTTGCATATGAGTATATT‑AC‑CCCCCCCCTCAAAAAAATAAATTAATTAAAATGATGGCTTATATAAAATAAAATTTAAAGc                                                                   >  1:1276850/1‑139 (MQ=255)

                     tGTTATGTCTTATCCCACGGTATTTAATATGGTTCATTAGGATGTTTATTTCTTGATTTTGCATATGAGTATATT‑AC‑CCCCCCCCTCAAAAAAATAAATTAATTAAAATGATGGCTTATATAAAATAAAATTTAAAGCa                                                                  <  2:1276850/139‑1 (MQ=255)

                         aTGTCTTATCCCACGGTATTTAATATGGTTCATTAGGATGTTTATTTCTTGATTTTGCATATGAGTATATT‑AC‑CCCCCCCCTCAAAAAAATAAATTAATTAAAatg                                                                                               >  1:212763/1‑106 (MQ=255)

                         aTGTCTTATCCCACGGTATTTAATATGGTTCATTAGGATGTTTATTTCTTGATTTTGCATATGAGTATATT‑AC‑CCCCCCCCTCAAAAAAATAAATTAATTAAAatg                                                                                               <  2:212763/106‑1 (MQ=255)

                                      cGGTATTTAATATGGTTCATTAGGATGTTTATTTCTTGATTTTGCATATGAGTATATT‑AC‑CCCCCCCCCCAAAAAAATAAATTAATTAAAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATg                                                 >  1:687741/1‑139 (MQ=255)

                                           tttAATATGGTTCATTAGGATGTTTATTTCTTGATTTTGCATATGAGTATATT‑AC‑CCCCCCCCTCAAAAAAATAAATTAATTAAAATGATGGCTTATATAAAATAAAATTTAAAGCAAGAAATCTCAATGGATGTTaaa                                            >  2:343155/1‑139 (MQ=255)

                                                     ttCATTAGGATGTTTATTTCTTGATTTTGCATATGAGTATATT‑AC‑CCCCCCCCTCAAAAAAATAAATTAATTAAAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATgaga                                  >  2:333871/1‑139 (MQ=255)

                                                     ttCATTAGGATGTTTATTTCTTGATTTTGCATATGAGTATATT‑AC‑CCCCCCCCTCAAAAAAATAAATTAATTAAAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATgaga                                  >  2:870322/1‑139 (MQ=255)

                                                              aTGTTTATTTCTTGATTTTGCATATGAGTATATT‑AC‑CCCCCCCCTCAAAAAAATAAATTAATTAAAatg                                                                                               >  1:1664332/1‑69 (MQ=255)

                                                              aTGTTTATTTCTTGATTTTGCATATGAGTATATT‑AC‑CCCCCCCCTCAAAAAAATAAATTAATTAAAatg                                                                                               <  2:1664332/69‑1 (MQ=255)

                                                               cgTTTATTTCTTGATTTTGCATATGAGTATATTAA‑‑ACCCCCCCTCCAAAAAATAAATTAATTAAAATGATGGCTTATATAAAATAAACTTAAAAGCAAGAAATCTCAATGGATGTTAAACAATATGAGATTTTGTGaaa                        >  1:63666/2‑139 (MQ=255)

                                                                           gATTTTGCATATGAGTATATT‑ACCCCCCCCCCTCAAAAAAATAAATTAATTAAAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAatta             >  1:1270112/1‑139 (MQ=255)

                                                                           gATTTTGCATATGAGTATATT‑AC‑CCCCCCCCTCAAAAAAATAAATTAATTAAAatg                                                                                               <  1:903511/56‑1 (MQ=255)

                                                                           gATTTTGCATATGAGTATATT‑AC‑CCCCCCCCTCAAAAAAATAAATTAATTAAAatg                                                                                               >  2:903511/1‑56 (MQ=255)

                                                                                     atGAATATTTT‑AC‑CCCCCCCCTCAAAAAAATAAATTAATTAAAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGtt  <  1:147856/139‑1 (MQ=255)

                                                                                          tataTT‑AC‑CCCCCCCCTCAAAAAAATAAATTAATTAAAatg                                                                                               >  1:263825/1‑41 (MQ=38)

                                                                                          tataTT‑AC‑CCCCCCCCTCAAAAAAATAAATTAATTAAAatg                                                                                               <  2:263825/41‑1 (MQ=38)

TCAATTACTATCCACTTCATTTGTTATGTCTTATCCCACGGTATTTAATATGGTTCATTAGGATGTTTATTTCTTGATTTTGCATATGAGTATATT‑A‑‑CCCCCCCCTCAAAAAAATAAATTAATTAAAATGATGGCTTATATAAAATAAAATTTAAAGCAAGGAATCTCAATGGATGTTAAACAAAATGAGATTTTGTGAAAGCAATAAATTATTGACTTCGTT  >  NC_000913/1211984‑1212206

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A