BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068927.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 = 1,861,119 number of mapped reads = 1,170,954 (62.92%) number of supplementary alignments = 5,878 (0.32%) number of secondary alignments = 0 number of mapped bases = 73,125,680 bp number of sequenced bases = 73,084,355 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 127,865 duplication rate = 9.05% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9788 >>>>>>> ACTG content number of A's = 19,052,196 bp (26.07%) number of C's = 12,144,247 bp (16.62%) number of T's = 24,940,690 bp (34.13%) number of G's = 16,788,689 bp (22.97%) number of N's = 158,533 bp (0.22%) GC percentage = 39.59% >>>>>>> Mismatches and indels general error rate = 0.0112 number of mismatches = 810,988 number of insertions = 6,374 mapped reads with insertion percentage = 0.54% number of deletions = 26,442 mapped reads with deletion percentage = 2.23% homopolymer indels = 48.84% >>>>>>> Coverage mean coverageData = 0.0236X std coverageData = 0.2633X There is a 1.58% of reference with a coverageData >= 1X There is a 0.46% of reference with a coverageData >= 2X There is a 0.18% 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% 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 7497886 0.030081714420282228 0.3964518532813224 chr2 243199373 6357094 0.026139434167044503 0.2762161301274 chr3 198022430 4656180 0.023513396941952484 0.21874665459138495 chr4 191154276 5032566 0.026327247840377894 0.2403288208028973 chr5 180915260 4695300 0.025953034586468825 0.23325098722215543 chr6 171115067 4205143 0.024574942895005267 0.25214416879207663 chr7 159138663 3681785 0.023135703986654706 0.29396833744215367 chr8 146364022 4366897 0.02983586362501025 0.35014219775175376 chr9 141213431 3091065 0.021889313063996017 0.25085554697189105 chr10 135534747 3317329 0.024475856364715096 0.253681254773177 chr11 135006516 3256809 0.024123346757574278 0.25153760729562535 chr12 133851895 3461516 0.025860791884941187 0.2350085264262089 chr13 115169878 2018449 0.01752584126207028 0.19007218758699773 chr14 107349540 1877324 0.01748795570060198 0.19388931928317404 chr15 102531392 1866697 0.0182061021857579 0.1968040068120507 chr16 90354753 1780270 0.019703114013271666 0.20525422631528104 chr17 81195210 1719065 0.021172000170946045 0.21823533336709022 chr18 78077248 1404011 0.017982332061703816 0.3440474766110436 chr19 59128983 1089814 0.01843113046608632 0.25956254289591957 chr20 63025520 1387286 0.022011496295468884 0.21434584214944066 chr21 48129895 962031 0.019988221457786268 0.20888702127613926 chr22 51304566 725345 0.014138020385943816 0.16760850955159426 chrMT 16571 88747 5.3555609196789575 4.712680322648847 chrX 155270560 4402798 0.028355652224091935 0.24926738717826327 chrY 59373566 184273 0.0031036202204866724 0.08419037334954711