BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549070.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 10,195,714 number of mapped reads = 8,862,742 (86.93%) number of secondary alignments = 0 number of mapped bases = 352,133,497 bp number of sequenced bases = 352,096,211 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 316,260 duplication rate = 2.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.9618 >>>>>>> ACTG content number of A's = 103,937,447 bp (29.52%) number of C's = 71,996,109 bp (20.45%) number of T's = 104,328,796 bp (29.63%) number of G's = 71,827,224 bp (20.4%) number of N's = 6,635 bp (0%) GC percentage = 40.85% >>>>>>> Mismatches and indels general error rate = 0.0031 number of mismatches = 1,079,872 number of insertions = 8,778 mapped reads with insertion percentage = 0.1% number of deletions = 28,959 mapped reads with deletion percentage = 0.33% homopolymer indels = 43.96% >>>>>>> Coverage mean coverageData = 0.1137X std coverageData = 0.9269X There is a 9.35% of reference with a coverageData >= 1X There is a 1.5% of reference with a coverageData >= 2X There is a 0.27% of reference with a coverageData >= 3X There is a 0.06% 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 0.01% 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 28872844 0.11583860406911484 2.035015231605696 chr2 243199373 30566610 0.12568539804582474 0.5837380905734288 chr3 198022430 23516122 0.11875484004514034 0.40004639099539246 chr4 191154276 24125347 0.12620877494783322 0.44391099382015203 chr5 180915260 22708896 0.12552228043118088 0.41785383501509904 chr6 171115067 21194990 0.12386396108532044 0.4933057303727196 chr7 159138663 19783953 0.12431895949760492 0.8162441580297195 chr8 146364022 18751971 0.12811871895676658 2.2782924044922823 chr9 141213431 14973723 0.10603611068695017 0.553341285704248 chr10 135534747 16797561 0.12393545841052848 0.6720150577571729 chr11 135006516 16418024 0.12160912292559271 0.5666588937258671 chr12 133851895 16278399 0.12161500589887055 0.4249585506344424 chr13 115169878 11946864 0.10373254020465317 0.36698982809021025 chr14 107349540 10983616 0.10231637694954258 0.418308797986943 chr15 102531392 10197222 0.09945463336731057 0.36044593746136805 chr16 90354753 9647924 0.1067782676579283 0.43128518894761797 chr17 81195210 8966716 0.11043405146682914 0.4243155885189399 chr18 78077248 9655106 0.12366094153318519 1.0673252899704548 chr19 59128983 6402766 0.10828473068782529 1.494598710165594 chr20 63025520 7261267 0.11521153653313769 0.40371062840556854 chr21 48129895 4665381 0.09693312233488147 0.4230541359202655 chr22 51304566 3857170 0.07518180740482241 0.34658596873881076 chrMT 16571 15480 0.9341620903988896 1.411718733383979 chrX 155270560 11551228 0.07439419294939105 0.3974766586114241 chrY 59373566 2994317 0.05043182011334808 0.4793328736686408