BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173903.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 3,807,734 number of mapped reads = 3,702,622 (97.24%) number of supplementary alignments = 383,707 (10.08%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,853,694 number of mapped paired reads (second in pair) = 1,848,928 number of mapped paired reads (both in pair) = 3,633,594 number of mapped paired reads (singletons) = 69,028 number of mapped bases = 438,093,157 bp number of sequenced bases = 437,828,290 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,928,595 duplication rate = 65.05% >>>>>>> Insert size mean insert size = 888,855.9694 std insert size = 8,772,567.0036 median insert size = 203 >>>>>>> Mapping quality mean mapping quality = 52.7092 >>>>>>> ACTG content number of A's = 131,816,885 bp (30.11%) number of C's = 85,616,945 bp (19.55%) number of T's = 131,563,708 bp (30.05%) number of G's = 88,825,333 bp (20.29%) number of N's = 5,419 bp (0%) GC percentage = 39.84% >>>>>>> Mismatches and indels general error rate = 0.0106 number of mismatches = 4,543,899 number of insertions = 44,902 mapped reads with insertion percentage = 1.18% number of deletions = 108,550 mapped reads with deletion percentage = 2.86% homopolymer indels = 42.16% >>>>>>> Coverage mean coverageData = 0.1415X std coverageData = 2.1263X There is a 2.85% of reference with a coverageData >= 1X There is a 2.27% of reference with a coverageData >= 2X There is a 1.77% of reference with a coverageData >= 3X There is a 1.47% of reference with a coverageData >= 4X There is a 1.14% of reference with a coverageData >= 5X There is a 0.94% of reference with a coverageData >= 6X There is a 0.71% of reference with a coverageData >= 7X There is a 0.58% of reference with a coverageData >= 8X There is a 0.43% of reference with a coverageData >= 9X There is a 0.36% of reference with a coverageData >= 10X There is a 0.26% of reference with a coverageData >= 11X There is a 0.22% of reference with a coverageData >= 12X There is a 0.17% of reference with a coverageData >= 13X There is a 0.15% of reference with a coverageData >= 14X There is a 0.11% of reference with a coverageData >= 15X There is a 0.1% of reference with a coverageData >= 16X There is a 0.07% of reference with a coverageData >= 17X There is a 0.06% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% 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 36626324 0.14694576829158632 1.7404240560136295 chr2 243199373 44695958 0.1837831958555255 6.026595552564663 chr3 198022430 31978263 0.16148808496088043 1.1920618460704366 chr4 191154276 21904396 0.11459014393170049 1.1582265925689526 chr5 180915260 30559707 0.1689172433547065 1.2155085865331041 chr6 171115067 23813146 0.13916451904261593 1.130923902468282 chr7 159138663 28468984 0.17889420121620603 1.7984017649433839 chr8 146364022 18746642 0.12808230973592677 1.2533532229516797 chr9 141213431 17759894 0.12576632317644063 1.1790816655841683 chr10 135534747 17600816 0.12986201981105258 2.066702909907442 chr11 135006516 20803508 0.15409262172205082 1.173401348360237 chr12 133851895 20624880 0.1540873216624987 1.1639696333890046 chr13 115169878 14570667 0.12651456485870377 1.063548507743248 chr14 107349540 10565720 0.09842352375240733 0.9275864506335387 chr15 102531392 14798838 0.1443347028781195 1.1128931801811264 chr16 90354753 17742417 0.19636395885006735 1.6724482773989033 chr17 81195210 10220735 0.12587854628370318 1.1031895571642605 chr18 78077248 6578501 0.08425631241510971 1.4595385126366038 chr19 59128983 8074826 0.1365629102736301 1.6733026599929859 chr20 63025520 14611827 0.23183984836618562 1.4148705213787995 chr21 48129895 6763540 0.14052679732627715 1.1347406605022836 chr22 51304566 3860758 0.07525174270063995 0.7713382663465461 chrMT 16571 942234 56.860418803934586 47.73963672435455 chrX 155270560 15170720 0.0977050639863732 0.9243877081803371 chrY 59373566 609856 0.010271507020481135 0.5370044796412855