BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926889.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 38,351,548 number of mapped reads = 35,904,899 (93.62%) number of supplementary alignments = 362,247 (0.94%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 17,997,767 number of mapped paired reads (second in pair) = 17,907,132 number of mapped paired reads (both in pair) = 35,556,876 number of mapped paired reads (singletons) = 348,023 number of mapped bases = 3,394,994,231 bp number of sequenced bases = 3,392,398,410 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,089,915 duplication rate = 6.85% >>>>>>> Insert size mean insert size = 82,468.9404 std insert size = 2,845,716.1377 median insert size = 170 >>>>>>> Mapping quality mean mapping quality = 53.4603 >>>>>>> ACTG content number of A's = 964,763,185 bp (28.44%) number of C's = 692,358,037 bp (20.41%) number of T's = 968,981,289 bp (28.56%) number of G's = 766,062,685 bp (22.58%) number of N's = 233,214 bp (0.01%) GC percentage = 42.99% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 31,421,140 number of insertions = 532,221 mapped reads with insertion percentage = 1.46% number of deletions = 1,846,434 mapped reads with deletion percentage = 5.01% homopolymer indels = 53.05% >>>>>>> Coverage mean coverageData = 1.0967X std coverageData = 4.8335X There is a 35.07% of reference with a coverageData >= 1X There is a 22.15% of reference with a coverageData >= 2X There is a 14.2% of reference with a coverageData >= 3X There is a 9.71% of reference with a coverageData >= 4X There is a 6.81% of reference with a coverageData >= 5X There is a 4.9% of reference with a coverageData >= 6X There is a 3.59% of reference with a coverageData >= 7X There is a 2.67% of reference with a coverageData >= 8X There is a 2.01% of reference with a coverageData >= 9X There is a 1.52% of reference with a coverageData >= 10X There is a 1.17% of reference with a coverageData >= 11X There is a 0.9% of reference with a coverageData >= 12X There is a 0.7% of reference with a coverageData >= 13X There is a 0.54% of reference with a coverageData >= 14X There is a 0.43% of reference with a coverageData >= 15X There is a 0.34% of reference with a coverageData >= 16X There is a 0.27% of reference with a coverageData >= 17X There is a 0.21% of reference with a coverageData >= 18X There is a 0.17% of reference with a coverageData >= 19X There is a 0.14% of reference with a coverageData >= 20X There is a 0.11% of reference with a coverageData >= 21X There is a 0.09% of reference with a coverageData >= 22X There is a 0.08% of reference with a coverageData >= 23X There is a 0.06% of reference with a coverageData >= 24X There is a 0.05% of reference with a coverageData >= 25X There is a 0.05% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% 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 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 282621790 1.133886001431467 3.9677083900960515 chr2 243199373 295571076 1.2153447287053656 6.072793780601075 chr3 198022430 228789376 1.1553710152935706 2.531348980269792 chr4 191154276 197980223 1.03570909917809 2.4389830034561655 chr5 180915260 202862838 1.1213141334788452 2.3308709810071577 chr6 171115067 190635536 1.1140780256363982 2.9187118381202106 chr7 159138663 175300704 1.1015594871498953 2.8851040630521285 chr8 146364022 167772956 1.1462718344812908 2.6271528361785883 chr9 141213431 148245704 1.049798896253714 4.484404287686693 chr10 135534747 174737701 1.2892465206726655 16.331270902090782 chr11 135006516 163937319 1.2142919012886755 3.0941067433364915 chr12 133851895 151667664 1.1331006109401738 2.554381040763156 chr13 115169878 99920677 0.8675938425496986 2.1345236044893663 chr14 107349540 102445615 0.9543181554387657 2.2763866963283235 chr15 102531392 102867647 1.0032795321846406 2.371049196007262 chr16 90354753 109968011 1.2170694661740706 6.663496894793704 chr17 81195210 91938456 1.1323137904317262 2.8306709896546516 chr18 78077248 88315030 1.1311237557963107 4.721385841305313 chr19 59128983 57656586 0.9750985569969975 2.829440879065137 chr20 63025520 83331497 1.3221865841011704 2.815727172871935 chr21 48129895 43028781 0.8940136063043561 3.0984934668204165 chr22 51304566 44040855 0.8584197944487046 2.310964335855734 chrMT 16571 39110 2.3601472451873757 2.504032487997531 chrX 155270560 186602703 1.2017906227684114 2.61099318393409 chrY 59373566 4716376 0.07943561954826833 1.6952582263845213