BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237580.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,569,942 number of mapped reads = 1,279,904 (81.53%) number of supplementary alignments = 6,849 (0.44%) number of secondary alignments = 0 number of mapped bases = 79,850,185 bp number of sequenced bases = 79,804,212 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 75,344 duplication rate = 4.11% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.4166 >>>>>>> ACTG content number of A's = 20,183,750 bp (25.29%) number of C's = 14,850,504 bp (18.61%) number of T's = 24,209,195 bp (30.34%) number of G's = 20,526,713 bp (25.72%) number of N's = 34,050 bp (0.04%) GC percentage = 44.33% >>>>>>> Mismatches and indels general error rate = 0.0097 number of mismatches = 759,357 number of insertions = 7,354 mapped reads with insertion percentage = 0.57% number of deletions = 28,202 mapped reads with deletion percentage = 2.17% homopolymer indels = 45.87% >>>>>>> Coverage mean coverageData = 0.0258X std coverageData = 0.2662X There is a 2.08% of reference with a coverageData >= 1X There is a 0.28% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 6956188 0.027908407899212416 0.312804188811272 chr2 243199373 7292333 0.02998499918007601 0.3734845912669757 chr3 198022430 5371081 0.02712359907915482 0.21483672389625652 chr4 191154276 4803587 0.025129372465620387 0.21905507790904954 chr5 180915260 4277692 0.023644727371256575 0.19373174808874258 chr6 171115067 4036385 0.0235887176434323 0.20966046882911504 chr7 159138663 4781293 0.030044823236952796 0.38702617186580346 chr8 146364022 4029424 0.02753015355098673 0.2570730062107385 chr9 141213431 3302206 0.023384503702059332 0.28757761468247056 chr10 135534747 3616140 0.02668053823865551 0.2547245482391723 chr11 135006516 3493525 0.02587671398023485 0.30017909580463487 chr12 133851895 4628204 0.03457705249522242 0.25104063319251424 chr13 115169878 2538156 0.02203836666389453 0.19436401364737282 chr14 107349540 2188264 0.020384474865937946 0.21203390735458993 chr15 102531392 2405903 0.023465037907609797 0.2063126296674987 chr16 90354753 2294070 0.025389588525575407 0.2270662177342633 chr17 81195210 2026232 0.024955068162272134 0.2229623650658428 chr18 78077248 1988405 0.025467150174145484 0.38056471832572 chr19 59128983 1653889 0.027970868364165843 0.27855210678614845 chr20 63025520 1777680 0.028205717303086113 0.2206601772918296 chr21 48129895 1045561 0.021723733243132985 0.20558297707009293 chr22 51304566 931961 0.01816526427686768 0.17710986101619983 chrMT 16571 61741 3.725846358095468 3.4694201121989408 chrX 155270560 4068415 0.026202101673362933 0.22225703226267826 chrY 59373566 281850 0.004747062017464136 0.11929472304815773