BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081741.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,182,253 number of mapped reads = 1,963,090 (89.96%) number of supplementary alignments = 16,052 (0.74%) number of secondary alignments = 0 number of mapped bases = 134,435,091 bp number of sequenced bases = 134,382,572 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 62,335 duplication rate = 2.3% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9932 >>>>>>> ACTG content number of A's = 38,819,969 bp (28.89%) number of C's = 25,476,673 bp (18.96%) number of T's = 41,453,727 bp (30.85%) number of G's = 28,630,630 bp (21.31%) number of N's = 1,573 bp (0%) GC percentage = 40.26% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,103,245 number of insertions = 11,025 mapped reads with insertion percentage = 0.55% number of deletions = 29,272 mapped reads with deletion percentage = 1.47% homopolymer indels = 47.04% >>>>>>> Coverage mean coverageData = 0.0434X std coverageData = 0.3698X There is a 3.79% of reference with a coverageData >= 1X There is a 0.4% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% 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 10385905 0.041668522061575924 0.5803123105350227 chr2 243199373 10066263 0.04139099075720068 0.4406838316848832 chr3 198022430 10220929 0.05161500644144201 0.2532488077660077 chr4 191154276 9836986 0.05146097804267795 0.29291783188119364 chr5 180915260 8243514 0.04556560900390603 0.23572470967030407 chr6 171115067 5925314 0.0346276578905819 0.2253870125914503 chr7 159138663 7804168 0.049040050059990764 0.4287877927740545 chr8 146364022 7895331 0.053943113151126716 0.6446295257410103 chr9 141213431 5720480 0.04050946117157935 0.3454498502738098 chr10 135534747 6571508 0.048485780550429625 0.44037579665790255 chr11 135006516 6305650 0.04670626416283492 0.3141039159638283 chr12 133851895 6768620 0.05056798037861175 0.2513101253775706 chr13 115169878 4958357 0.043052550598343085 0.22801251392554372 chr14 107349540 3179586 0.029618999764693916 0.20918575523104804 chr15 102531392 4143135 0.04040845363730164 0.22332222452325562 chr16 90354753 4007737 0.044355574742149975 0.28026882653440593 chr17 81195210 3352463 0.041288925787617274 0.23015068138139871 chr18 78077248 3565495 0.04566624838006585 0.6236388698284624 chr19 59128983 2435731 0.041193520950630926 0.4295510904478455 chr20 63025520 2594369 0.0411637857172777 0.2330590004962583 chr21 48129895 1783601 0.03705806962595701 0.24662892560621963 chr22 51304566 1232187 0.024017102103543766 0.17059242813653103 chrMT 16571 13844 0.8354353991913585 1.0715432274633463 chrX 155270560 7051579 0.04541478436092457 0.2608256453786115 chrY 59373566 372339 0.006271124089127475 0.19593646051542196