BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173934.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 = 7,415,316 number of mapped reads = 7,236,592 (97.59%) number of supplementary alignments = 1,018,552 (13.74%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,620,733 number of mapped paired reads (second in pair) = 3,615,859 number of mapped paired reads (both in pair) = 7,124,110 number of mapped paired reads (singletons) = 112,482 number of mapped bases = 817,678,320 bp number of sequenced bases = 817,048,880 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,803,029 duplication rate = 64.12% >>>>>>> Insert size mean insert size = 965,417.796 std insert size = 9,228,494.734 median insert size = 155 >>>>>>> Mapping quality mean mapping quality = 52.3908 >>>>>>> ACTG content number of A's = 243,791,494 bp (29.84%) number of C's = 161,966,355 bp (19.82%) number of T's = 242,191,467 bp (29.64%) number of G's = 169,093,518 bp (20.7%) number of N's = 6,046 bp (0%) GC percentage = 40.52% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 7,274,999 number of insertions = 91,195 mapped reads with insertion percentage = 1.21% number of deletions = 270,156 mapped reads with deletion percentage = 3.64% homopolymer indels = 40.22% >>>>>>> Coverage mean coverageData = 0.2641X std coverageData = 4.8657X There is a 5.74% of reference with a coverageData >= 1X There is a 4.28% of reference with a coverageData >= 2X There is a 3.18% of reference with a coverageData >= 3X There is a 2.55% of reference with a coverageData >= 4X There is a 1.9% of reference with a coverageData >= 5X There is a 1.57% of reference with a coverageData >= 6X There is a 1.17% of reference with a coverageData >= 7X There is a 1.01% of reference with a coverageData >= 8X There is a 0.76% of reference with a coverageData >= 9X There is a 0.67% of reference with a coverageData >= 10X There is a 0.5% of reference with a coverageData >= 11X There is a 0.46% of reference with a coverageData >= 12X There is a 0.34% of reference with a coverageData >= 13X There is a 0.31% of reference with a coverageData >= 14X There is a 0.23% of reference with a coverageData >= 15X There is a 0.21% of reference with a coverageData >= 16X There is a 0.16% of reference with a coverageData >= 17X There is a 0.15% of reference with a coverageData >= 18X There is a 0.11% of reference with a coverageData >= 19X There is a 0.1% of reference with a coverageData >= 20X There is a 0.08% of reference with a coverageData >= 21X There is a 0.07% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% 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 0.01% 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 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% 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 65781256 0.26391611678271404 2.357676162765078 chr2 243199373 75048003 0.3085863342254587 15.968892471527816 chr3 198022430 55910692 0.2823452474550484 1.5940947103189715 chr4 191154276 56056130 0.29325072487523113 2.237364422666142 chr5 180915260 50044057 0.27661600795864316 1.5691612378832296 chr6 171115067 48423687 0.28298903100099304 1.904764643794118 chr7 159138663 44990282 0.28271119759250457 2.36804945643266 chr8 146364022 41377131 0.28270015017761674 2.5790693824520408 chr9 141213431 35107856 0.2486155583883519 2.012370831780015 chr10 135534747 39996365 0.2951004512518107 2.8760009157207347 chr11 135006516 38035778 0.28173290539546997 1.6508924364946274 chr12 133851895 36513295 0.2727887789709664 1.6374887538933027 chr13 115169878 27379354 0.23773016413197903 1.4654555679605388 chr14 107349540 25571776 0.23821039195882907 1.4876648376771147 chr15 102531392 23623999 0.23040747364475458 1.485598505322371 chr16 90354753 24829155 0.2747963352852063 1.9819020617873755 chr17 81195210 22711243 0.27971161106671194 1.7059368385109526 chr18 78077248 22145349 0.2836338314588137 2.851995855705914 chr19 59128983 15797134 0.2671639727001562 1.8640874583581768 chr20 63025520 17741560 0.2814980344469986 1.6687290765710907 chr21 48129895 11513789 0.2392232312162742 1.9291141502886007 chr22 51304566 10177241 0.1983691081218775 1.5751324033032676 chrMT 16571 807598 48.73562247299499 41.4344326656092 chrX 155270560 21683149 0.139647522363544 1.1256268084284862 chrY 59373566 6412441 0.10800161472531396 1.7521694855872925