BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524328.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 = 768,640 number of mapped reads = 703,310 (91.5%) number of supplementary alignments = 3,078 (0.4%) number of secondary alignments = 0 number of mapped bases = 41,018,957 bp number of sequenced bases = 41,008,031 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,667 duplication rate = 1.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.9902 >>>>>>> ACTG content number of A's = 10,014,104 bp (24.42%) number of C's = 7,487,385 bp (18.26%) number of T's = 12,689,245 bp (30.94%) number of G's = 10,811,555 bp (26.36%) number of N's = 5,742 bp (0.01%) GC percentage = 44.62% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 211,245 number of insertions = 2,786 mapped reads with insertion percentage = 0.39% number of deletions = 7,000 mapped reads with deletion percentage = 0.99% homopolymer indels = 41.24% >>>>>>> Coverage mean coverageData = 0.0133X std coverageData = 0.1508X There is a 1.25% of reference with a coverageData >= 1X There is a 0.05% 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 3490258 0.014003006235238227 0.2345524653722543 chr2 243199373 2607800 0.010722889487054722 0.1830341533649561 chr3 198022430 2695479 0.013611988298497297 0.12229360185364979 chr4 191154276 2148859 0.011241490616720496 0.11767480046921495 chr5 180915260 2443089 0.013504051565357174 0.12100540604227836 chr6 171115067 2551640 0.014911837073938089 0.133117051781864 chr7 159138663 1935902 0.012164875357787819 0.1784353914976141 chr8 146364022 4247213 0.029018149009324163 0.20314337097466093 chr9 141213431 1717836 0.012164820214587096 0.12812569126472165 chr10 135534747 2105573 0.015535300331508347 0.15714119639568766 chr11 135006516 1968230 0.0145787778124724 0.14044707292581302 chr12 133851895 1624654 0.012137698909679239 0.11557452192875728 chr13 115169878 1048490 0.009103856131548564 0.0997579328457768 chr14 107349540 851621 0.007933159285079377 0.09480480670329622 chr15 102531392 1298063 0.012660151926933753 0.11675747517998548 chr16 90354753 1300373 0.014391860492386051 0.12841072594062405 chr17 81195210 1245059 0.015334143479646152 0.13426032522529496 chr18 78077248 946847 0.012127053965836502 0.18205274220847983 chr19 59128983 753541 0.012744020982062215 0.18737421465005613 chr20 63025520 972775 0.01543462076949147 0.1307031065278825 chr21 48129895 593100 0.012322902428937358 0.11950819389823762 chr22 51304566 308365 0.006010478677472879 0.08078004568002813 chrMT 16571 2660 0.16052139279464125 0.4019304313450223 chrX 155270560 2038909 0.013131330240581343 0.1263439512470991 chrY 59373566 122621 0.002065245668417491 0.07155997888470064