BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525130.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 = 1,829,076 number of mapped reads = 1,689,337 (92.36%) number of supplementary alignments = 44,725 (2.45%) number of secondary alignments = 0 number of mapped bases = 130,537,126 bp number of sequenced bases = 130,485,148 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 58,218 duplication rate = 2.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1296 >>>>>>> ACTG content number of A's = 35,108,862 bp (26.91%) number of C's = 25,125,950 bp (19.26%) number of T's = 39,260,391 bp (30.09%) number of G's = 30,984,941 bp (23.75%) number of N's = 5,004 bp (0%) GC percentage = 43% >>>>>>> Mismatches and indels general error rate = 0.0073 number of mismatches = 925,799 number of insertions = 10,867 mapped reads with insertion percentage = 0.63% number of deletions = 30,066 mapped reads with deletion percentage = 1.75% homopolymer indels = 42.79% >>>>>>> Coverage mean coverageData = 0.0422X std coverageData = 0.4599X There is a 3.66% of reference with a coverageData >= 1X There is a 0.37% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 12657990 0.0507841864113149 0.8374110152614074 chr2 243199373 10918372 0.044894737454771315 0.6247223951485877 chr3 198022430 8288223 0.04185497067175673 0.2285847535214438 chr4 191154276 8385581 0.04386813193757696 0.24209657823962258 chr5 180915260 7799443 0.04311102888722599 0.23535997333732675 chr6 171115067 7268471 0.0424770952519336 0.2644352278977661 chr7 159138663 6894648 0.04332478273994297 0.649401001744005 chr8 146364022 6569230 0.04488281963172616 0.6016953140822034 chr9 141213431 5356464 0.03793168937308803 0.42171844985374013 chr10 135534747 5996246 0.04424139294700569 0.4467299714729217 chr11 135006516 7157505 0.05301599665011724 0.5271583748372832 chr12 133851895 5715813 0.04270251833192201 0.23205880615660418 chr13 115169878 4816636 0.0418220118284748 0.22870165072822288 chr14 107349540 3787144 0.0352786234575388 0.25970487818940413 chr15 102531392 3517992 0.034311364854970466 0.2051704301765945 chr16 90354753 2833144 0.03135578268915195 0.22966764094192135 chr17 81195210 3690789 0.04545574794375185 0.2957299821357192 chr18 78077248 3511120 0.0449698227068659 0.7926989953979086 chr19 59128983 2410335 0.040764019228945646 0.5693237433228991 chr20 63025520 2417428 0.038356335655778805 0.22679357985274873 chr21 48129895 1650953 0.03430202787685284 0.2267763622216415 chr22 51304566 1284716 0.02504096808849333 0.17423324647602137 chrMT 16571 51766 3.123891135115563 3.204984882077449 chrX 155270560 7270737 0.04682624317191875 0.3446082929962052 chrY 59373566 286380 0.004823358596989105 0.11387344153867895