BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173916.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 = 2,342,342 number of mapped reads = 2,278,970 (97.29%) number of supplementary alignments = 230,137 (9.83%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,141,573 number of mapped paired reads (second in pair) = 1,137,397 number of mapped paired reads (both in pair) = 2,235,810 number of mapped paired reads (singletons) = 43,160 number of mapped bases = 269,652,793 bp number of sequenced bases = 269,507,397 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,758,528 duplication rate = 64.36% >>>>>>> Insert size mean insert size = 918,659.0604 std insert size = 9,004,046.7723 median insert size = 203 >>>>>>> Mapping quality mean mapping quality = 52.7253 >>>>>>> ACTG content number of A's = 80,831,207 bp (29.99%) number of C's = 52,925,022 bp (19.64%) number of T's = 80,783,994 bp (29.97%) number of G's = 54,964,225 bp (20.39%) number of N's = 2,949 bp (0%) GC percentage = 40.03% >>>>>>> Mismatches and indels general error rate = 0.0105 number of mismatches = 2,769,401 number of insertions = 27,369 mapped reads with insertion percentage = 1.17% number of deletions = 60,679 mapped reads with deletion percentage = 2.6% homopolymer indels = 43.05% >>>>>>> Coverage mean coverageData = 0.0871X std coverageData = 1.455X There is a 1.89% of reference with a coverageData >= 1X There is a 1.48% of reference with a coverageData >= 2X There is a 1.13% of reference with a coverageData >= 3X There is a 0.92% of reference with a coverageData >= 4X There is a 0.69% of reference with a coverageData >= 5X There is a 0.55% of reference with a coverageData >= 6X There is a 0.41% of reference with a coverageData >= 7X There is a 0.33% of reference with a coverageData >= 8X There is a 0.24% of reference with a coverageData >= 9X There is a 0.2% of reference with a coverageData >= 10X There is a 0.14% of reference with a coverageData >= 11X There is a 0.12% of reference with a coverageData >= 12X There is a 0.09% of reference with a coverageData >= 13X There is a 0.08% of reference with a coverageData >= 14X There is a 0.06% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% 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% 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 22398736 0.08986431371819932 1.3110302003849228 chr2 243199373 26403768 0.10856840490291889 3.933239923948872 chr3 198022430 20290359 0.10246495308637511 0.9157629444795563 chr4 191154276 16480423 0.08621529868366638 0.8912920519214625 chr5 180915260 19085736 0.10549544576836692 0.9312411295552196 chr6 171115067 15630886 0.09134722192523234 0.8733474700457696 chr7 159138663 19223571 0.12079761534756642 1.3971144038306897 chr8 146364022 10983870 0.07504487680722521 0.8129370437724749 chr9 141213431 9134240 0.06468393222454881 0.7837977506775348 chr10 135534747 13209883 0.09746491798151215 1.3943014349736766 chr11 135006516 13251376 0.09815360319349327 0.9081701201379636 chr12 133851895 9229541 0.06895338314037316 0.7418395023497478 chr13 115169878 8495882 0.07376826430258092 0.7795971918793768 chr14 107349540 8245713 0.07681181493651487 0.783045635189881 chr15 102531392 8796150 0.085789823276758 0.8267978034099631 chr16 90354753 10576191 0.11705185005596773 1.1515575024661762 chr17 81195210 6303255 0.07763087256009314 0.8190833119674878 chr18 78077248 4451090 0.05700879723629603 1.106592849020517 chr19 59128983 4984080 0.08429165778143013 1.2859137213525411 chr20 63025520 6115203 0.09702741048388018 0.8735198799519881 chr21 48129895 4192074 0.0870991719387711 0.8503649913222191 chr22 51304566 2344291 0.04569361331309186 0.5705732471667376 chrMT 16571 796712 48.078691690302335 40.58155336881375 chrX 155270560 8690755 0.055971685810883916 0.6727832351482469 chrY 59373566 339008 0.005709746320441659 0.26929224143661373