BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173859.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 = 2,074,964 number of mapped reads = 2,022,808 (97.49%) number of supplementary alignments = 194,179 (9.36%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,011,151 number of mapped paired reads (second in pair) = 1,011,657 number of mapped paired reads (both in pair) = 1,988,906 number of mapped paired reads (singletons) = 33,902 number of mapped bases = 238,456,318 bp number of sequenced bases = 238,325,356 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,548,968 duplication rate = 64.68% >>>>>>> Insert size mean insert size = 1,082,296.0825 std insert size = 9,833,279.0033 median insert size = 188 >>>>>>> Mapping quality mean mapping quality = 53.0559 >>>>>>> ACTG content number of A's = 71,957,263 bp (30.19%) number of C's = 46,606,129 bp (19.56%) number of T's = 71,604,961 bp (30.05%) number of G's = 48,154,077 bp (20.21%) number of N's = 2,926 bp (0%) GC percentage = 39.76% >>>>>>> Mismatches and indels general error rate = 0.0104 number of mismatches = 2,393,904 number of insertions = 26,553 mapped reads with insertion percentage = 1.27% number of deletions = 52,717 mapped reads with deletion percentage = 2.53% homopolymer indels = 43.4% >>>>>>> Coverage mean coverageData = 0.077X std coverageData = 1.2929X There is a 1.67% of reference with a coverageData >= 1X There is a 1.31% of reference with a coverageData >= 2X There is a 0.99% of reference with a coverageData >= 3X There is a 0.81% of reference with a coverageData >= 4X There is a 0.61% of reference with a coverageData >= 5X There is a 0.49% of reference with a coverageData >= 6X There is a 0.36% of reference with a coverageData >= 7X There is a 0.29% of reference with a coverageData >= 8X There is a 0.21% of reference with a coverageData >= 9X There is a 0.18% of reference with a coverageData >= 10X There is a 0.13% of reference with a coverageData >= 11X There is a 0.11% of reference with a coverageData >= 12X There is a 0.08% of reference with a coverageData >= 13X There is a 0.07% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.03% 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% 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 19161292 0.0768756038525577 0.9697181981621621 chr2 243199373 21651768 0.0890288808433729 3.502391967678263 chr3 198022430 16698378 0.08432568977160819 0.8359994599325227 chr4 191154276 16045697 0.08394108327453789 0.9970714958892094 chr5 180915260 14743258 0.08149261704070734 0.8197643059101258 chr6 171115067 13936812 0.08144701833883512 0.8530860180249943 chr7 159138663 14027321 0.0881452736598648 0.9494271651549387 chr8 146364022 13720907 0.09374508033128524 1.1321877612027869 chr9 141213431 10118685 0.07165525919414846 0.8839151923962173 chr10 135534747 11429666 0.08433015335912347 1.0862681549098325 chr11 135006516 10529272 0.07799084304938289 0.7999636809082028 chr12 133851895 10408269 0.07775959391534949 0.7967684665421739 chr13 115169878 7712889 0.06696967239993082 0.7413682772400841 chr14 107349540 7529129 0.0701365744091684 0.7580114206058405 chr15 102531392 6670721 0.06506027929475491 0.7305014198749106 chr16 90354753 6909940 0.07647566697459734 0.8250604338556942 chr17 81195210 6537362 0.08051413377710336 0.8112964669551889 chr18 78077248 5987248 0.07668364540717419 1.0201486246555467 chr19 59128983 3847066 0.0650622724223077 0.7665935280934233 chr20 63025520 5839320 0.09265008840863193 0.8697538514460269 chr21 48129895 3256105 0.06765244345536178 0.8405593837658748 chr22 51304566 2581074 0.050308855550985465 0.639090059922625 chrMT 16571 351535 21.213867600024138 20.269273190949196 chrX 155270560 7110842 0.04579646006300228 0.6169511097903625 chrY 59373566 1651762 0.02781982136629624 0.6169184963005983