BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525115.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 = 2,239,373 number of mapped reads = 2,038,606 (91.03%) number of supplementary alignments = 8,509 (0.38%) number of secondary alignments = 0 number of mapped bases = 116,801,417 bp number of sequenced bases = 116,769,130 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 82,559 duplication rate = 3.05% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4218 >>>>>>> ACTG content number of A's = 28,339,819 bp (24.27%) number of C's = 23,867,121 bp (20.44%) number of T's = 37,111,875 bp (31.78%) number of G's = 27,446,699 bp (23.51%) number of N's = 3,616 bp (0%) GC percentage = 43.94% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 565,340 number of insertions = 7,675 mapped reads with insertion percentage = 0.37% number of deletions = 19,479 mapped reads with deletion percentage = 0.95% homopolymer indels = 41.78% >>>>>>> Coverage mean coverageData = 0.0377X std coverageData = 0.3289X There is a 3.31% of reference with a coverageData >= 1X There is a 0.34% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 9149060 0.03670626762450473 0.6311900179765706 chr2 243199373 9876457 0.04061053644246032 0.3501496897257911 chr3 198022430 7725363 0.039012565394738366 0.21842129884063596 chr4 191154276 7687362 0.040215485422884285 0.24502844640283486 chr5 180915260 7337620 0.040558325483433515 0.2253842348718827 chr6 171115067 6803884 0.03976203918968749 0.2446838496020708 chr7 159138663 6635140 0.041694079081209826 0.36359394088779756 chr8 146364022 6026354 0.04117373872111823 0.3854499429979384 chr9 141213431 5067406 0.035884731106065965 0.3164693046682419 chr10 135534747 5533288 0.04082560466948007 0.31062259819317145 chr11 135006516 5445747 0.040336919738007314 0.29892088568107833 chr12 133851895 5355174 0.04000820459060367 0.2306450430542891 chr13 115169878 3802160 0.033013493337207496 0.20125666973017808 chr14 107349540 3460841 0.032238992360842905 0.22355479452645177 chr15 102531392 1802678 0.017581717802095186 0.1494796877930896 chr16 90354753 3584659 0.03967316473102417 0.24013275835216905 chr17 81195210 3198476 0.039392422286979735 0.23460450381780298 chr18 78077248 3333538 0.04269538291103703 0.5221021384390806 chr19 59128983 2279919 0.03855840037025497 0.45633678349122686 chr20 63025520 2587079 0.041048118286053016 0.2318296527631598 chr21 48129895 1535093 0.03189479220762896 0.22825380743695212 chr22 51304566 1343932 0.026195173349678077 0.17879128238250103 chrMT 16571 46257 2.7914428821435036 2.36451482301577 chrX 155270560 6855534 0.0441521818431002 0.2737257886452124 chrY 59373566 328396 0.005531013582711202 0.1313129494484998