BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716290.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 715,583 number of mapped reads = 622,643 (87.01%) number of supplementary alignments = 1,767 (0.25%) number of secondary alignments = 0 number of mapped bases = 35,043,563 bp number of sequenced bases = 35,032,999 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,676 duplication rate = 1.2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.5163 >>>>>>> ACTG content number of A's = 7,999,973 bp (22.84%) number of C's = 7,681,032 bp (21.93%) number of T's = 10,233,930 bp (29.21%) number of G's = 9,117,084 bp (26.02%) number of N's = 980 bp (0%) GC percentage = 47.95% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 184,997 number of insertions = 2,810 mapped reads with insertion percentage = 0.45% number of deletions = 6,221 mapped reads with deletion percentage = 0.99% homopolymer indels = 37.83% >>>>>>> Coverage mean coverageData = 0.0113X std coverageData = 0.1261X There is a 1.06% of reference with a coverageData >= 1X There is a 0.05% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% 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 3318722 0.013314799324010512 0.1464677405226748 chr2 243199373 2912296 0.011974932188661523 0.16264786724091718 chr3 198022430 2251735 0.01137111083830251 0.11538382721568947 chr4 191154276 2171044 0.011357548705842185 0.12482201948749723 chr5 180915260 2928868 0.016189170554214167 0.13406782644844253 chr6 171115067 1454750 0.008501589167481085 0.09874269091359138 chr7 159138663 1971111 0.012386122660839497 0.13783966620133037 chr8 146364022 2022540 0.013818559864390718 0.1286212566510197 chr9 141213431 1478232 0.010468069428891646 0.1141967561458078 chr10 135534747 1776982 0.013110896204351198 0.16126527755270792 chr11 135006516 1405589 0.010411267853175324 0.12350170878051442 chr12 133851895 1567262 0.011708926496707425 0.11457639579808485 chr13 115169878 580006 0.005036091120978699 0.07511193973380927 chr14 107349540 1456749 0.013570146644317247 0.12424593525898533 chr15 102531392 683865 0.006669810939463301 0.08645867471120736 chr16 90354753 953826 0.010556456282936217 0.11725512300503602 chr17 81195210 1384592 0.017052631553018952 0.14202610709088379 chr18 78077248 864546 0.011072956874709518 0.13020147547176406 chr19 59128983 969856 0.01640237918517895 0.1481742689204849 chr20 63025520 864154 0.013711176044243665 0.12665834319620028 chr21 48129895 456647 0.009487803785983743 0.11016319400185155 chr22 51304566 377158 0.007351353483820524 0.09149834485786205 chrMT 16571 648 0.039104459598093055 0.20503885868175126 chrX 155270560 1073611 0.0069144530682442315 0.09228697639232626 chrY 59373566 118774 0.0020004525246133946 0.07100729932510895