BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174005.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 = 3,427,264 number of mapped reads = 3,356,538 (97.94%) number of supplementary alignments = 273,399 (7.98%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,678,579 number of mapped paired reads (second in pair) = 1,677,959 number of mapped paired reads (both in pair) = 3,310,870 number of mapped paired reads (singletons) = 45,668 number of mapped bases = 399,466,821 bp number of sequenced bases = 399,239,627 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,528,817 duplication rate = 64.82% >>>>>>> Insert size mean insert size = 665,097.6801 std insert size = 7,409,298.1689 median insert size = 200 >>>>>>> Mapping quality mean mapping quality = 52.9778 >>>>>>> ACTG content number of A's = 121,640,907 bp (30.47%) number of C's = 76,977,950 bp (19.28%) number of T's = 121,303,387 bp (30.38%) number of G's = 79,312,313 bp (19.87%) number of N's = 5,070 bp (0%) GC percentage = 39.15% >>>>>>> Mismatches and indels general error rate = 0.0104 number of mismatches = 4,029,685 number of insertions = 41,965 mapped reads with insertion percentage = 1.21% number of deletions = 90,384 mapped reads with deletion percentage = 2.62% homopolymer indels = 43.39% >>>>>>> Coverage mean coverageData = 0.129X std coverageData = 2.0161X There is a 2.8% of reference with a coverageData >= 1X There is a 2.2% of reference with a coverageData >= 2X There is a 1.67% of reference with a coverageData >= 3X There is a 1.36% of reference with a coverageData >= 4X There is a 1.02% of reference with a coverageData >= 5X There is a 0.82% of reference with a coverageData >= 6X There is a 0.6% of reference with a coverageData >= 7X There is a 0.48% of reference with a coverageData >= 8X There is a 0.35% of reference with a coverageData >= 9X There is a 0.29% of reference with a coverageData >= 10X There is a 0.21% of reference with a coverageData >= 11X There is a 0.18% of reference with a coverageData >= 12X There is a 0.13% of reference with a coverageData >= 13X There is a 0.11% of reference with a coverageData >= 14X There is a 0.08% of reference with a coverageData >= 15X There is a 0.07% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.05% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% 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 0.01% 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 0.01% of reference with a coverageData >= 29X There is a 0.01% 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 31756670 0.12740858928491897 1.799682331855255 chr2 243199373 39354515 0.16181996900131812 5.4038343188949645 chr3 198022430 33441231 0.16887597531249365 1.1759076619005957 chr4 191154276 26018236 0.13611119010489725 1.2214394582334005 chr5 180915260 28480138 0.1574225303050721 1.1321939217619155 chr6 171115067 24012167 0.1403276018937596 1.0998964725756846 chr7 159138663 27152268 0.1706201842351786 2.2897805500051396 chr8 146364022 17311837 0.11827932003672323 1.148801847443334 chr9 141213431 15293271 0.10829898326031041 1.1081331698113883 chr10 135534747 18429245 0.1359743195595444 2.5832437199970886 chr11 135006516 17573327 0.13016650988904863 1.0401859664964221 chr12 133851895 15429355 0.11527184579643045 0.9722913731432028 chr13 115169878 12177814 0.10573783884706381 0.9185836540501662 chr14 107349540 12592775 0.1173062781638375 0.9768328963624179 chr15 102531392 12059323 0.11761591025702646 0.9662408011604969 chr16 90354753 15106515 0.16719114931341797 1.6557423023395372 chr17 81195210 7881535 0.09706896502884838 0.9932601762486687 chr18 78077248 5892434 0.07546928395836902 1.3810931890442135 chr19 59128983 6576375 0.1112208373345437 1.763552062730683 chr20 63025520 10657852 0.16910375352714266 1.1525035613067207 chr21 48129895 6025256 0.12518739132923518 1.0323270598468928 chr22 51304566 2843145 0.05541699738771789 0.6261565907647877 chrMT 16571 845426 51.01840564842194 44.90193737721461 chrX 155270560 12046686 0.077585126246727 0.7817783045189166 chrY 59373566 509425 0.008579996694151737 0.4482422335977366