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
A2 F1 I0 R1	4577	57.4	3436498	77.7%	2670158	63.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	1,973,145	A→G	26.4%	intergenic (‑85/‑36)	yqgB ← / → yqgC	hypothetical protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,973,145	0	A	G	26.4%	51.6 / 16.6	49	intergenic (‑85/‑36)	yqgB/yqgC	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand): ref base A (17/19); new base G (7/6); total (24/25)
Fisher's exact test for biased strand distribution p-value = 7.54e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.76e-01

AAAGTTCGGCGAAACCACGAGAAAACTCTTGTTTTTACAAGAGCGCCCTTGTTCAGTCCTCAGTAACTGTAACCAGCTCTTGAATCCTGAGAAGCGCCGAGATGGGTATAACATCGGCAGGTATGCAAAGCAGA  >  minE/1973080‑1973213

aaaGTTCGGCGAAACCACGAGAAAACTCTTGTTTTTACAAGAGCGCCCTT‑TTCAGTCCTCAGTAACTGt                                                                  <  1:2601420/69‑1 (MQ=255)

  aGTTCGGCGAAACCACGAGAAAACTCTTGTTTTTACAAGAGCGCCCTTGTTCAGTCCTCAGTAACTGt                                                                  <  1:3027411/68‑1 (MQ=255)

  aGTTCGGCGAAACCACGAGAAAACTCTTGTTTTTACAAGAGCGCCCTTGTTCAGTCCTCAGTAACTGt                                                                  <  1:2278031/68‑1 (MQ=255)

            aaCCACGAGAAAACTCTTGTTTTTACAAGAGCGCCCTTGTTCAGTCCTCAGTAGCTGTAACCAGCTCtt                                                       <  1:1016008/69‑1 (MQ=255)

            aaCCACGAGAAAACTCTTGTTTTTACAAGAGCGCCCTTGTTCAGTCCTCAGTAGCTGTAACCAGCTCtt                                                       <  1:653865/69‑1 (MQ=255)

            aaCCACGAGAAAACTCTTGTTTTTACAAGAGCGCCCTTGTTCAGTCCTCAGTAGCTGTAACCAGCTCtt                                                       <  1:643246/69‑1 (MQ=255)

            aaCCACGAGAAAACTCTTGTTTTTACAAGAGCGCCCTTGTTCAGTCCTCAGTAGCTGTAACCAGCTCtt                                                       <  1:1365559/69‑1 (MQ=255)

            aaCCACGAGAAAACTCTTGTTTTTACAAGAGCGCCCTTGTTCAGTCCTCAGTAGCTGTAACCAGCTCtt                                                       <  1:33375/69‑1 (MQ=255)

            aaCCACGAGAAAACTCTTGTTTTTACAAGAGCGCCCTTGTTCAGTCCTCAGTAGCTGTAACCAGCTCtt                                                       <  1:3016992/69‑1 (MQ=255)

                aCGAGAAAACTCTTGTTTTTACAAGAGCGCCCTTGTTCAGTCCTCAGTAACTGTAACCAGCTCTTGAAt                                                   >  1:2160945/1‑69 (MQ=255)

                       aaCTCTTGTTTTTACAAGAGCGCCCTTGTTCAGTCCTCAGTAACTGTAACCAGCTCTTGAATCCTgaga                                            >  1:9954/1‑69 (MQ=255)

                       aaCTCTTGTTTTTACAAGAGCGCCCTTGTTCAGTCCTCAGTAACTGTAACCAGCTCTTGAATCCTgaga                                            >  1:1003265/1‑69 (MQ=255)

                       aaCTCTTGTTTTTACAAGAGCGCCCTTGTTCAGTCCTCAGTAACTGTAACCAGCTCTTGAATCCTgaga                                            >  1:2458987/1‑69 (MQ=255)

                       aaCTCTTGTTTTTACAAGAGCGCCCTTGTTCAGTCCTCAGTAACTGTAACCAGCTCTTGAATCCTgaga                                            >  1:2251520/1‑69 (MQ=255)

                       aaCTCTTGTTTTTACAAGAGCGCCCTTGTTCAGTCCTCAGTAACTGTAACCAGCTCTTGAATCCTgaga                                            >  1:1230735/1‑69 (MQ=255)

                       aaCTCTTGTTTTTACAAGAGCGCCCTTGTTCAGTCCTCAGTAACTGTAACCAGCTCTTGAATCCTga                                              >  1:2117648/1‑67 (MQ=255)

                             tGTTTTTACAAGAGCGCCCTTGTTCAGTCCTCAGTAGCTGTAACCAGctc                                                         >  1:1028839/1‑50 (MQ=255)

                             tGTTTTTACAAGAGCGCCCTTGTTCAGTCCTCAGTAGCTGTAACCAGctc                                                         >  1:2895327/1‑50 (MQ=255)

                             tGTTTTTACAAGAGCGCCCTTGTTCAGTCCTCAGTAGCTGTAACCAGctc                                                         >  1:2659621/1‑50 (MQ=255)

                             tGTTTTTACAAGAGCGCCCTTGTTCAGTCCTCAGTAGCTGTAACCAGctc                                                         >  1:577575/1‑50 (MQ=255)

                             tGTTTTTACAAGAGCGCCCTTGTTCAGTCCTCAGTAGCTGTAACCAGctc                                                         >  1:2302569/1‑50 (MQ=255)

                             tGTTTTTACAAGAGCGCCCTTGTTCAGTCCTCAGTAGCTGTAACCAGctc                                                         >  1:3307262/1‑50 (MQ=255)

                             tGTTTTTACAAGAGCGCCCTTGTTCAGTCCTCAGTAGCTGTAAACAGctc                                                         >  1:1877095/1‑50 (MQ=255)

                                ttttACAAGAGCGCCCTTGTTCAGTCCTCAGTAACTGTAACCAGCTCTTGTATCCTGAGAAGCGCCga                                    <  1:1717033/68‑1 (MQ=255)

                                ttttACAAGAGCGCCCTTGTTCAGTCCTCAGTAACTGTAACCAGCTCTTGAATCCTGAGAAGCGCCga                                    <  1:3215638/68‑1 (MQ=255)

                                ttttACAAGAGCGCCCTTGTTCAGTCCTCAGTAACTGTAACCAGCTCTTGAATCCTGAGAAGCGCCga                                    <  1:1751044/68‑1 (MQ=255)

                                ttttACAAGAGCGCCCTTGTTCAGTCCTCAGTAACTGTAACCAGCTCTTGAATCCTGAGAAGCGCCga                                    <  1:297806/68‑1 (MQ=255)

                                ttttACAAGAGCGCCCTTGTTCAGTCCTCAGTAACTGTAACCAGCTCTTGAATCCTGAGAAGCGCCga                                    <  1:2996414/68‑1 (MQ=255)

                                 tttACAAGAGCGCCCTTGTTCAGTCCTCAGTAACTGTAACCAGCTCTTGAATCCTGAGAAGCGCCgag                                   <  1:3340665/68‑1 (MQ=255)

                                 tttACAAGAGCGCCCTTGTTCAGTCCTCAGTAACTGTAACCAGCTCTTGAATCCTGAGAAGCGCCgag                                   <  1:70219/68‑1 (MQ=255)

                                             cccTTGTTCAGTCCTCAGTAACTGTAACCAGCTCTTGAATCCTGAGAAGCGCCGAGATGGGTATAACAt                      >  1:569165/1‑69 (MQ=255)

                                             cccTTGTTCAGTCCTCAGTAACTGTAACCAGCTCTTGAATCCTGAGAAGCGCCGAGATGGGTATAACAt                      >  1:1435594/1‑69 (MQ=255)

                                             cccTTGTTCAGTCCTCAGTAACTGTAACCAGCTCTTGAATCCTGAGAAGCGCCGAGATGGGTATAACAt                      >  1:2513345/1‑69 (MQ=255)

                                             cccTTGTTCAGTCCTCAGTAACTGTAACCAGCTCTTGAATCCTGAGAAGCGCCGAGATGGGTATAACAt                      >  1:1577393/1‑69 (MQ=255)

                                             cccTTGTTCAGTCCTCAGTAACTGTAACCAGCTCTTGAATCCTGAGAAGCGCCGAGATGGGAATAACAt                      >  1:2334602/1‑69 (MQ=255)

                                                 tGTTCAGTCCTCAGTAACTGTAACCAGCTCTTGAATCCTGAGAAGCGCCgag                                   <  1:453610/52‑1 (MQ=255)

                                                 tGTTCAGTCCTCAGTAACTGTAACCAGCTCTTGAATCCTGAGAAGCGCCga                                    <  1:411861/51‑1 (MQ=255)

                                                 tGTTCAGTCCTCAGTAACTGTAACCAGCTCTTGAATCCTGAGAAGCGCCGAGATGGGTATAACATCGGc                  <  1:306500/69‑1 (MQ=255)

                                                 tGTTCAGTCCTCAGTAACTGTAACCAGCTCTTGAATCCTGAGAAGCGCCGAGATGGGTATAACATCGGc                  <  1:991873/69‑1 (MQ=255)

                                                 tGTTCAGTCCTCAGTAACTGTAACCAGCTCTTGAATCCTGAGAAGCGCCGAGATGGGTATAACATCGGc                  <  1:2088834/69‑1 (MQ=255)

                                                 tGTTCAGTCCTCAGTAACTGTAACCAGCTCTTGAATCCTGAGAAGCGCCGAGATGGGTATAACATCGGc                  <  1:1403689/69‑1 (MQ=255)

                                                     cAGTCCTCAGTAACTGTAACCAGCTCTTGAATCCTGAGAAGCGCCGAGATGGGTATAACATCGGCAgg               <  1:2500186/68‑1 (MQ=255)

                                                     cAGTCCTCAGTAACTGTAACCAGCTCTTGAATCCTGAGAAGCGCCGAGATGGGTATAACATCGGCAGGt              <  1:524339/69‑1 (MQ=255)

                                                          cTCAGTAACTGTAACCAGCTCTTGAATCCTGAGAAGCGCCGAGATGGGTATAACATCGGCAGGTATGCa         <  1:3223724/69‑1 (MQ=255)

                                                            cAGTAACTGTAACCAGCTCTTGAATCCTGAGAAGCGCCGAGATGGGTATAACATCGGCAGGTATGCaa        >  1:1748060/1‑68 (MQ=255)

                                                            cAGTAACTGTAACCAGCTCTTGAATCCTGAGAAGCGCCGAGATGGGTATAACATCGGCAGGTATGCaa        >  1:1253657/1‑68 (MQ=255)

                                                            cAGTAACTGTAACCAGCTCTTGAATCCTGAGAAGCGCCGAGATGGGTATAACATCGGCAGGTATGCaa        >  1:1809365/1‑68 (MQ=255)

                                                            cAGTAACTGTAACCAGCTCTTGAATCCTGAGAAGCGCCGAGATGGGTATAACATCGGCAGGTATGCaa        >  1:833655/1‑68 (MQ=255)

                                                             aGTAACTGTAACCAGCTCTTGAATCCTGAGAAGCGCCGAGATGGGTATAACATCGGCAGATATGCaa        >  1:1974982/1‑67 (MQ=255)

                                                                 aCTGTAACCAGCTCTTGAATCCTGAGAAGCGCCGAGATGGGTATAACATCGGCAGGTATGCAAAGCagt  >  1:1615917/1‑68 (MQ=255)

AAAGTTCGGCGAAACCACGAGAAAACTCTTGTTTTTACAAGAGCGCCCTTGTTCAGTCCTCAGTAACTGTAACCAGCTCTTGAATCCTGAGAAGCGCCGAGATGGGTATAACATCGGCAGGTATGCAAAGCAGA  >  minE/1973080‑1973213

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A