BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524792.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 = 1,246,183 number of mapped reads = 1,133,718 (90.98%) number of supplementary alignments = 4,701 (0.38%) number of secondary alignments = 0 number of mapped bases = 64,889,402 bp number of sequenced bases = 64,868,016 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 41,684 duplication rate = 2.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3395 >>>>>>> ACTG content number of A's = 16,192,276 bp (24.96%) number of C's = 11,440,519 bp (17.64%) number of T's = 20,464,436 bp (31.55%) number of G's = 16,763,272 bp (25.84%) number of N's = 7,513 bp (0.01%) GC percentage = 43.48% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 332,276 number of insertions = 4,249 mapped reads with insertion percentage = 0.37% number of deletions = 13,141 mapped reads with deletion percentage = 1.15% homopolymer indels = 42.7% >>>>>>> Coverage mean coverageData = 0.021X std coverageData = 0.2018X There is a 1.89% of reference with a coverageData >= 1X There is a 0.15% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 5146083 0.020646219372909808 0.274603812624601 chr2 243199373 5501044 0.02261948265795899 0.30025127269229346 chr3 198022430 4313073 0.021780729587047284 0.16188247209480766 chr4 191154276 4152029 0.02172082721288432 0.18092252096873385 chr5 180915260 3874977 0.02141874046445833 0.15878303773004848 chr6 171115067 3624863 0.02118377454160714 0.16963580294421643 chr7 159138663 3541609 0.02225486210098422 0.23597885144211114 chr8 146364022 3273481 0.022365339208839177 0.19257673602626077 chr9 141213431 2737506 0.019385592295395753 0.17409366631689002 chr10 135534747 3189193 0.023530445664977705 0.24742075546886444 chr11 135006516 2945802 0.02181970239125347 0.18069732511659864 chr12 133851895 2915051 0.02177818252031471 0.16209763303524688 chr13 115169878 2024779 0.01758080355003936 0.14407328706360945 chr14 107349540 1955369 0.018214973254659497 0.14985701202409166 chr15 102531392 1845188 0.017996322531152215 0.14766695957880635 chr16 90354753 1960746 0.021700529688792353 0.172439682913384 chr17 81195210 1840664 0.02266961314589863 0.16897252636720136 chr18 78077248 1661903 0.021285368562170635 0.2506998990998758 chr19 59128983 1414867 0.023928485291214968 0.22404788130990688 chr20 63025520 1448601 0.02298435617825922 0.17065609917750227 chr21 48129895 852052 0.017703175957479233 0.15697841738636978 chr22 51304566 815484 0.015894959524655174 0.1383790577210778 chrMT 16571 16433 0.9916721984189246 1.1499397376559728 chrX 155270560 3608426 0.023239601892335548 0.17599172835584892 chrY 59373566 230179 0.003876792578030432 0.11762380707015412