BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173981.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 = 3,438,454 number of mapped reads = 3,371,525 (98.05%) number of supplementary alignments = 454,404 (13.22%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,686,403 number of mapped paired reads (second in pair) = 1,685,122 number of mapped paired reads (both in pair) = 3,330,622 number of mapped paired reads (singletons) = 40,903 number of mapped bases = 382,119,623 bp number of sequenced bases = 381,845,671 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,718,426 duplication rate = 65.29% >>>>>>> Insert size mean insert size = 955,446.1353 std insert size = 9,178,971.8455 median insert size = 151 >>>>>>> Mapping quality mean mapping quality = 52.4257 >>>>>>> ACTG content number of A's = 114,005,618 bp (29.86%) number of C's = 75,850,329 bp (19.86%) number of T's = 113,324,321 bp (29.68%) number of G's = 78,662,495 bp (20.6%) number of N's = 2,908 bp (0%) GC percentage = 40.46% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 3,261,902 number of insertions = 46,285 mapped reads with insertion percentage = 1.32% number of deletions = 120,473 mapped reads with deletion percentage = 3.49% homopolymer indels = 40.99% >>>>>>> Coverage mean coverageData = 0.1234X std coverageData = 2.2163X There is a 2.66% of reference with a coverageData >= 1X There is a 1.98% of reference with a coverageData >= 2X There is a 1.46% of reference with a coverageData >= 3X There is a 1.18% of reference with a coverageData >= 4X There is a 0.88% of reference with a coverageData >= 5X There is a 0.74% of reference with a coverageData >= 6X There is a 0.55% of reference with a coverageData >= 7X There is a 0.48% of reference with a coverageData >= 8X There is a 0.36% of reference with a coverageData >= 9X There is a 0.33% of reference with a coverageData >= 10X There is a 0.24% of reference with a coverageData >= 11X There is a 0.23% of reference with a coverageData >= 12X There is a 0.17% of reference with a coverageData >= 13X There is a 0.15% of reference with a coverageData >= 14X There is a 0.11% of reference with a coverageData >= 15X There is a 0.11% of reference with a coverageData >= 16X There is a 0.08% 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 0.02% of reference with a coverageData >= 25X There is a 0.02% 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 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% 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 24108859 0.0967253718497255 1.3303313191807296 chr2 243199373 31351333 0.12891206343693987 6.603355658175241 chr3 198022430 22201673 0.11211696068975621 1.0135557229334795 chr4 191154276 31815639 0.16643958830405656 1.652966502032438 chr5 180915260 24644844 0.1362231356271439 1.1268910255186726 chr6 171115067 32573626 0.19036094583067895 1.4780405496915001 chr7 159138663 20605966 0.12948434787340146 1.4361379045580853 chr8 146364022 24430644 0.16691700368824244 1.5699955202063043 chr9 141213431 15895048 0.1125604546779973 1.3347077298316143 chr10 135534747 19588261 0.14452575028601336 1.7503186995172604 chr11 135006516 10186733 0.0754536395858108 0.8981365909929515 chr12 133851895 18662372 0.13942553446852582 1.142373017947839 chr13 115169878 10417656 0.09045469337043147 0.9171140642455398 chr14 107349540 10180565 0.09483566487569485 0.946905936007933 chr15 102531392 8325047 0.08119510364201434 0.8753059598575236 chr16 90354753 8411654 0.09309586624623942 1.0457303367747375 chr17 81195210 10065357 0.12396491123060092 1.125309713334563 chr18 78077248 12199827 0.15625329161191748 1.647536634301025 chr19 59128983 10122641 0.1711959260317398 1.3167366042854838 chr20 63025520 8656715 0.13735253592513 1.1808792201178822 chr21 48129895 4890408 0.10160853249316251 1.1152389982495283 chr22 51304566 4919502 0.09588819053649143 0.9104308562956671 chrMT 16571 363409 21.930420614326234 23.667195055941043 chrX 155270560 15488454 0.09975138880158609 0.9643409791828274 chrY 59373566 2013390 0.03391054530900165 0.910751889828177