BamQC report ----------------------------------- >>>>>>> Input bam file = SRR22354874.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP408873/SRP408873.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 = 23,349,652 number of mapped reads = 23,082,198 (98.85%) number of supplementary alignments = 1,486,936 (6.37%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 11,553,266 number of mapped paired reads (second in pair) = 11,528,932 number of mapped paired reads (both in pair) = 23,038,358 number of mapped paired reads (singletons) = 43,840 number of mapped bases = 2,667,100,269 bp number of sequenced bases = 2,665,714,502 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,654,005 duplication rate = 61.57% >>>>>>> Insert size mean insert size = 662,270.7172 std insert size = 9,441,948.432 median insert size = 129 >>>>>>> Mapping quality mean mapping quality = 53.1475 >>>>>>> ACTG content number of A's = 710,105,435 bp (26.64%) number of C's = 579,996,116 bp (21.76%) number of T's = 722,483,764 bp (27.1%) number of G's = 653,050,761 bp (24.5%) number of N's = 78,426 bp (0%) GC percentage = 46.26% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 15,030,814 number of insertions = 446,047 mapped reads with insertion percentage = 1.79% number of deletions = 452,477 mapped reads with deletion percentage = 1.86% homopolymer indels = 41.96% >>>>>>> Coverage mean coverageData = 0.8616X std coverageData = 73.2778X There is a 23.83% of reference with a coverageData >= 1X There is a 19.52% of reference with a coverageData >= 2X There is a 10.64% of reference with a coverageData >= 3X There is a 8.95% of reference with a coverageData >= 4X There is a 4.79% of reference with a coverageData >= 5X There is a 4.08% of reference with a coverageData >= 6X There is a 2.18% of reference with a coverageData >= 7X There is a 1.86% of reference with a coverageData >= 8X There is a 1.01% of reference with a coverageData >= 9X There is a 0.85% of reference with a coverageData >= 10X There is a 0.48% of reference with a coverageData >= 11X There is a 0.4% of reference with a coverageData >= 12X There is a 0.24% of reference with a coverageData >= 13X There is a 0.2% of reference with a coverageData >= 14X There is a 0.13% of reference with a coverageData >= 15X There is a 0.11% of reference with a coverageData >= 16X There is a 0.07% of reference with a coverageData >= 17X There is a 0.07% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 211958498 0.8503830287347609 22.44640069756188 chr2 243199373 270803428 1.1135038082520057 257.3246014495515 chr3 198022430 169623498 0.8565872967016919 3.2065351687010186 chr4 191154276 172912719 0.9045715461787525 14.850066801963788 chr5 180915260 152906173 0.8451811804045717 2.1505279823482795 chr6 171115067 142500829 0.8327777997480491 3.2291391148736888 chr7 159138663 145899988 0.9168104422242129 22.478461677418352 chr8 146364022 126658472 0.8653661621843106 3.6055910718059883 chr9 141213431 114186014 0.8086059037826225 10.789502191265676 chr10 135534747 151040764 1.1144062120099727 36.232917497547774 chr11 135006516 121800724 0.9021840397688656 5.1990205044674465 chr12 133851895 113601860 0.8487131243080271 2.020220473083619 chr13 115169878 75959199 0.6595405006854309 1.7177443731519835 chr14 107349540 78649230 0.7326461762202241 10.324205357921674 chr15 102531392 76527628 0.7463824152509312 1.8411431157202205 chr16 90354753 90258873 0.998938849403971 7.175450641993544 chr17 81195210 79871973 0.9837030164710455 5.57301723058915 chr18 78077248 69185462 0.8861155300965525 11.00541468352534 chr19 59128983 60761795 1.0276144103476295 12.422802595564725 chr20 63025520 57662495 0.9149070884302105 4.902899232081338 chr21 48129895 37823234 0.7858573969463262 7.726733262553648 chr22 51304566 36316987 0.7078704651745812 3.0558985710522855 chrMT 16571 3751713 226.40232937058718 69.59911256742274 chrX 155270560 70724293 0.45549068026804307 2.21740602606502 chrY 59373566 35714420 0.6015205487236526 18.937055254509836