BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524405.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 = 857,216 number of mapped reads = 793,950 (92.62%) number of supplementary alignments = 2,995 (0.35%) number of secondary alignments = 0 number of mapped bases = 46,442,906 bp number of sequenced bases = 46,430,518 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 21,996 duplication rate = 2.13% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.93 >>>>>>> ACTG content number of A's = 11,153,002 bp (24.02%) number of C's = 9,067,620 bp (19.53%) number of T's = 14,414,575 bp (31.05%) number of G's = 11,789,438 bp (25.39%) number of N's = 5,883 bp (0.01%) GC percentage = 44.92% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 224,641 number of insertions = 2,653 mapped reads with insertion percentage = 0.33% number of deletions = 7,992 mapped reads with deletion percentage = 1% homopolymer indels = 43.35% >>>>>>> Coverage mean coverageData = 0.015X std coverageData = 0.1654X There is a 1.4% of reference with a coverageData >= 1X There is a 0.07% 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 3166272 0.012703165943165293 0.2704879307018363 chr2 243199373 4007105 0.016476625538010742 0.18976759984150732 chr3 198022430 3142664 0.015870242578075625 0.1320155059971767 chr4 191154276 3030284 0.01585255670660488 0.14363544939119824 chr5 180915260 2845608 0.0157289550920138 0.13209359559718123 chr6 171115067 2591593 0.015145323234452522 0.13697350540855063 chr7 159138663 2654060 0.01667765676779627 0.2103330900535137 chr8 146364022 2435741 0.01664166484848305 0.1625240504915598 chr9 141213431 2054115 0.014546173019477164 0.15070465412338593 chr10 135534747 2111203 0.015576839494893512 0.1544980672617593 chr11 135006516 2121242 0.0157121453308224 0.15571245232799824 chr12 133851895 2019790 0.015089737803114405 0.1309167098651434 chr13 115169878 1499109 0.013016502457352608 0.1203430549731442 chr14 107349540 1347077 0.012548512084914384 0.12053923648012607 chr15 102531392 1409971 0.01375160302124836 0.12298357859428724 chr16 90354753 1445516 0.015998228670936657 0.13706649121031342 chr17 81195210 1317799 0.016230009134775316 0.1408958853504482 chr18 78077248 1243387 0.015925087421114023 0.24048255317419684 chr19 59128983 954142 0.016136621189645695 0.19211509871412508 chr20 63025520 1018012 0.016152377640041685 0.13617645226797148 chr21 48129895 625997 0.013006406932738997 0.12902307374058594 chr22 51304566 567007 0.011051784357750926 0.11058335827418517 chrMT 16571 4069 0.24554945386518617 0.5821484553820518 chrX 155270560 2686378 0.017301270762467784 0.14589394256731053 chrY 59373566 144765 0.002438206254951909 0.07315300434680727