BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525112.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 818,233 number of mapped reads = 737,464 (90.13%) number of supplementary alignments = 21,987 (2.69%) number of secondary alignments = 0 number of mapped bases = 56,518,515 bp number of sequenced bases = 56,495,513 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 15,932 duplication rate = 1.3% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4431 >>>>>>> ACTG content number of A's = 14,794,852 bp (26.19%) number of C's = 11,429,852 bp (20.23%) number of T's = 16,947,792 bp (30%) number of G's = 13,320,830 bp (23.58%) number of N's = 2,187 bp (0%) GC percentage = 43.81% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 418,911 number of insertions = 5,718 mapped reads with insertion percentage = 0.76% number of deletions = 13,116 mapped reads with deletion percentage = 1.75% homopolymer indels = 41.94% >>>>>>> Coverage mean coverageData = 0.0183X std coverageData = 0.2052X There is a 1.7% of reference with a coverageData >= 1X There is a 0.08% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% 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 4535387 0.018196091074132167 0.2992152896553252 chr2 243199373 4688468 0.019278289833419924 0.28649505242907214 chr3 198022430 3583198 0.01809490975340521 0.1409995785572468 chr4 191154276 3532572 0.018480214379300624 0.15016457738065195 chr5 180915260 3436781 0.018996634114778376 0.1454339073662681 chr6 171115067 3288348 0.01921717390321917 0.1592552711430528 chr7 159138663 3206640 0.02014997449111408 0.2957036907781875 chr8 146364022 2822322 0.01928289453537974 0.2582901063145887 chr9 141213431 2463795 0.017447313492439682 0.19778897753090932 chr10 135534747 2672743 0.01971998368802061 0.2085940177839931 chr11 135006516 2525708 0.01870804517316779 0.19730826090798367 chr12 133851895 2636693 0.01969858551498281 0.14735685453915032 chr13 115169878 1745625 0.015156957967776956 0.1283500625886112 chr14 107349540 1729272 0.01610879748529896 0.13936098374734854 chr15 102531392 1614111 0.015742603006891783 0.13128084648167804 chr16 90354753 1693763 0.018745698967269603 0.15198887781886078 chr17 81195210 1607583 0.01979898814228081 0.1648820004651118 chr18 78077248 1519197 0.019457614592153658 0.2894228576355474 chr19 59128983 1238806 0.020950909979290527 0.2500563547057497 chr20 63025520 1202657 0.019082063900464446 0.14823430616097621 chr21 48129895 750338 0.015589853250251222 0.1388096049793729 chr22 51304566 673668 0.013130761110034533 0.1196006402167203 chrMT 16571 2689 0.16227143805443245 0.43326276043607886 chrX 155270560 3190541 0.020548267488698438 0.17422441209877257 chrY 59373566 157610 0.0026545483220596854 0.07734533915360624