BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716738.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 = 1,595,808 number of mapped reads = 1,461,336 (91.57%) number of supplementary alignments = 8,590 (0.54%) number of secondary alignments = 0 number of mapped bases = 85,365,804 bp number of sequenced bases = 85,340,518 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 51,961 duplication rate = 2.55% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6823 >>>>>>> ACTG content number of A's = 22,116,078 bp (25.92%) number of C's = 15,978,351 bp (18.72%) number of T's = 26,022,203 bp (30.49%) number of G's = 21,222,784 bp (24.87%) number of N's = 1,102 bp (0%) GC percentage = 43.59% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 428,961 number of insertions = 5,569 mapped reads with insertion percentage = 0.38% number of deletions = 16,003 mapped reads with deletion percentage = 1.09% homopolymer indels = 41.09% >>>>>>> Coverage mean coverageData = 0.0276X std coverageData = 0.2718X There is a 2.47% of reference with a coverageData >= 1X There is a 0.2% of reference with a coverageData >= 2X There is a 0.03% 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 6364833 0.025535876197475955 0.3420283113722355 chr2 243199373 8400609 0.034542066849818726 0.31598240760202434 chr3 198022430 6464885 0.0326472359722078 0.20741089579666513 chr4 191154276 4706852 0.024623315253486665 0.19804987834027707 chr5 180915260 4317375 0.02386407315778669 0.16841114963414439 chr6 171115067 4737508 0.027686094994779156 0.19554512427837162 chr7 159138663 5312932 0.0333855513163385 0.6026219935652531 chr8 146364022 7087991 0.04842714010687681 0.33071481895647026 chr9 141213431 3566395 0.02525535265834593 0.19557614383979105 chr10 135534747 4128765 0.030462778670328722 0.3596440095945486 chr11 135006516 2916480 0.021602512874267493 0.1926984823106204 chr12 133851895 3649095 0.027262184072926274 0.20220263646767003 chr13 115169878 2201614 0.019116231068682734 0.14971981641548984 chr14 107349540 2142990 0.01996273109321195 0.1578409487577506 chr15 102531392 2031641 0.01981481925067398 0.15510555091698264 chr16 90354753 2648719 0.029314661509837782 0.19532454301922347 chr17 81195210 3646789 0.04491384405557914 0.24160181832608493 chr18 78077248 1984941 0.025422783856316248 0.2993834797201256 chr19 59128983 1746042 0.0295293764819192 0.3195863053471653 chr20 63025520 1775731 0.028174793321816306 0.1909992155844593 chr21 48129895 893382 0.01856189380841159 0.16625138324484542 chr22 51304566 1336809 0.0260563358044974 0.1758514144490135 chrMT 16571 87920 5.305654456580774 4.134754399222936 chrX 155270560 2995137 0.019289793248636444 0.17105801271633186 chrY 59373566 220369 0.003711567534953181 0.10854876267999355