BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514712.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP106579/SRP106579.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 = 48,292,808 number of mapped reads = 47,281,298 (97.91%) number of supplementary alignments = 3,788,932 (7.85%) number of secondary alignments = 0 number of mapped bases = 4,444,777,593 bp number of sequenced bases = 4,441,100,367 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 45,900,096 duplication rate = 51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.3553 >>>>>>> ACTG content number of A's = 1,269,629,995 bp (28.59%) number of C's = 942,960,769 bp (21.23%) number of T's = 1,265,860,012 bp (28.5%) number of G's = 961,527,947 bp (21.65%) number of N's = 1,121,644 bp (0.03%) GC percentage = 42.88% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 32,685,779 number of insertions = 2,286,801 mapped reads with insertion percentage = 4.67% number of deletions = 1,404,073 mapped reads with deletion percentage = 2.85% homopolymer indels = 38.27% >>>>>>> Coverage mean coverageData = 1.4358X std coverageData = 271.1535X There is a 2.63% of reference with a coverageData >= 1X There is a 1.06% of reference with a coverageData >= 2X There is a 0.62% of reference with a coverageData >= 3X There is a 0.48% of reference with a coverageData >= 4X There is a 0.41% of reference with a coverageData >= 5X There is a 0.37% of reference with a coverageData >= 6X There is a 0.34% of reference with a coverageData >= 7X There is a 0.32% of reference with a coverageData >= 8X There is a 0.3% of reference with a coverageData >= 9X There is a 0.29% of reference with a coverageData >= 10X There is a 0.28% of reference with a coverageData >= 11X There is a 0.27% of reference with a coverageData >= 12X There is a 0.26% of reference with a coverageData >= 13X There is a 0.25% of reference with a coverageData >= 14X There is a 0.25% of reference with a coverageData >= 15X There is a 0.24% of reference with a coverageData >= 16X There is a 0.23% of reference with a coverageData >= 17X There is a 0.23% of reference with a coverageData >= 18X There is a 0.22% of reference with a coverageData >= 19X There is a 0.22% of reference with a coverageData >= 20X There is a 0.22% of reference with a coverageData >= 21X There is a 0.21% of reference with a coverageData >= 22X There is a 0.21% of reference with a coverageData >= 23X There is a 0.21% of reference with a coverageData >= 24X There is a 0.2% of reference with a coverageData >= 25X There is a 0.2% of reference with a coverageData >= 26X There is a 0.2% of reference with a coverageData >= 27X There is a 0.19% of reference with a coverageData >= 28X There is a 0.19% of reference with a coverageData >= 29X There is a 0.19% of reference with a coverageData >= 30X There is a 0.19% of reference with a coverageData >= 31X There is a 0.18% of reference with a coverageData >= 32X There is a 0.18% of reference with a coverageData >= 33X There is a 0.18% of reference with a coverageData >= 34X There is a 0.18% of reference with a coverageData >= 35X There is a 0.17% of reference with a coverageData >= 36X There is a 0.17% of reference with a coverageData >= 37X There is a 0.17% of reference with a coverageData >= 38X There is a 0.17% of reference with a coverageData >= 39X There is a 0.17% of reference with a coverageData >= 40X There is a 0.17% of reference with a coverageData >= 41X There is a 0.16% of reference with a coverageData >= 42X There is a 0.16% of reference with a coverageData >= 43X There is a 0.16% of reference with a coverageData >= 44X There is a 0.16% of reference with a coverageData >= 45X There is a 0.16% of reference with a coverageData >= 46X There is a 0.16% of reference with a coverageData >= 47X There is a 0.16% of reference with a coverageData >= 48X There is a 0.15% of reference with a coverageData >= 49X There is a 0.15% of reference with a coverageData >= 50X There is a 0.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 441597422 1.7717003882610187 181.97179125186148 chr2 243199373 553807161 2.277173473633914 610.9280552866456 chr3 198022430 201460718 1.0173631239653003 51.256579701480455 chr4 191154276 180798927 0.9458272699063243 47.35052372099177 chr5 180915260 298522874 1.6500701709739687 93.01505084715632 chr6 171115067 198598457 1.160613501089299 58.11964958113584 chr7 159138663 181163364 1.1383994347118525 77.4563112319663 chr8 146364022 216425575 1.47868015679427 129.0406278191226 chr9 141213431 173192985 1.2264625522766315 78.57190997626107 chr10 135534747 186345062 1.3748877400420425 110.11704356715636 chr11 135006516 421692664 3.1234986020971016 881.3034244557335 chr12 133851895 131775348 0.9844862338332976 52.218712446391336 chr13 115169878 156574754 1.3595113298635255 98.56107193357118 chr14 107349540 150797724 1.4047356327749518 95.3486547559815 chr15 102531392 224395460 2.1885537260627457 229.20888514303678 chr16 90354753 70572867 0.7810642457292756 60.62976860689796 chr17 81195210 77975114 0.9603413058479682 41.221239152443616 chr18 78077248 84964083 1.0882054013993936 49.19376529783506 chr19 59128983 32978448 0.5577374466257943 30.152836296620016 chr20 63025520 165915631 2.6325150669125774 226.11357901681765 chr21 48129895 39604803 0.8228732474899436 47.49416002890799 chr22 51304566 76034765 1.4820272527010558 94.35296006199586 chrMT 16571 260230 15.703940619153943 41.86406121093656 chrX 155270560 127432968 0.8207155818849369 121.09848200699962 chrY 59373566 51890189 0.8739611328044538 41.37158237278394