BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063541.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 3,776,858 number of mapped reads = 3,418,524 (90.51%) number of supplementary alignments = 24,857 (0.66%) number of secondary alignments = 0 number of mapped bases = 221,923,362 bp number of sequenced bases = 221,825,158 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 194,777 duplication rate = 4.32% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.5793 >>>>>>> ACTG content number of A's = 59,849,911 bp (26.98%) number of C's = 40,702,777 bp (18.35%) number of T's = 69,967,281 bp (31.54%) number of G's = 51,300,787 bp (23.13%) number of N's = 4,402 bp (0%) GC percentage = 41.48% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 1,752,999 number of insertions = 16,487 mapped reads with insertion percentage = 0.48% number of deletions = 60,935 mapped reads with deletion percentage = 1.76% homopolymer indels = 45.72% >>>>>>> Coverage mean coverageData = 0.0717X std coverageData = 0.6308X There is a 5.62% of reference with a coverageData >= 1X There is a 1.07% of reference with a coverageData >= 2X There is a 0.24% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 21306651 0.0854828401811685 1.1426249424353345 chr2 243199373 24111992 0.09914495955546727 1.0165375345995142 chr3 198022430 13201067 0.06666450361204031 0.3152837028909898 chr4 191154276 15425267 0.08069538031155526 0.36151402714727243 chr5 180915260 9613527 0.05313828695268713 0.2838059458086386 chr6 171115067 16687168 0.09752015583759202 0.504565162591346 chr7 159138663 10966008 0.06890850905288805 0.7434638585561417 chr8 146364022 8702523 0.05945807501791663 0.938007035375592 chr9 141213431 6167278 0.043673451996219824 0.5485646729166997 chr10 135534747 12506342 0.0922740645983572 0.5183808379484404 chr11 135006516 7193693 0.05328404297167405 0.3989234170201622 chr12 133851895 10907056 0.08148600361616098 0.3722313844717076 chr13 115169878 6515623 0.05657402016176487 0.29668986104713346 chr14 107349540 5925752 0.055200534627349127 0.36164900553979173 chr15 102531392 1828972 0.017838166090634953 0.22357952996675837 chr16 90354753 6084304 0.06733795177327306 0.36025451043649526 chr17 81195210 5657234 0.06967447956597439 0.34530112896265847 chr18 78077248 6156513 0.07885156249359608 0.8879966147555579 chr19 59128983 4911587 0.08306564312124225 0.8677675486077862 chr20 63025520 4579442 0.07266012243929126 0.36090196049658285 chr21 48129895 4906212 0.10193689389931143 0.40950083189438424 chr22 51304566 2154230 0.04198905025334392 0.24620491582180665 chrMT 16571 26571 1.6034638826866212 1.8814647858220337 chrX 155270560 15781227 0.10163695551816133 0.48723551381641356 chrY 59373566 607123 0.010225476435085607 0.18762532077942914