BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081198.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 = 4,286,687 number of mapped reads = 3,443,172 (80.32%) number of supplementary alignments = 36,431 (0.85%) number of secondary alignments = 0 number of mapped bases = 228,657,002 bp number of sequenced bases = 228,577,420 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 291,858 duplication rate = 6.07% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0668 >>>>>>> ACTG content number of A's = 64,258,362 bp (28.11%) number of C's = 44,879,360 bp (19.63%) number of T's = 68,552,646 bp (29.99%) number of G's = 49,773,737 bp (21.78%) number of N's = 1,113,315 bp (0.49%) GC percentage = 41.41% >>>>>>> Mismatches and indels general error rate = 0.0136 number of mismatches = 3,077,251 number of insertions = 16,152 mapped reads with insertion percentage = 0.47% number of deletions = 49,923 mapped reads with deletion percentage = 1.43% homopolymer indels = 46.55% >>>>>>> Coverage mean coverageData = 0.0739X std coverageData = 0.7976X There is a 4.92% of reference with a coverageData >= 1X There is a 1.49% of reference with a coverageData >= 2X There is a 0.5% of reference with a coverageData >= 3X There is a 0.18% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% 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 0.01% 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 23164578 0.09293689182022138 1.7863614263506233 chr2 243199373 13758251 0.056571901606012776 0.652203720423874 chr3 198022430 13964717 0.07052088493207562 0.39048303124456374 chr4 191154276 9291959 0.04860973656691833 0.33504888393876137 chr5 180915260 16080548 0.08888442025288525 0.42075005338617477 chr6 171115067 15382550 0.08989594119143231 0.5679735412146655 chr7 159138663 14399639 0.09048485596488894 1.1217694988745937 chr8 146364022 13610354 0.09298975126551251 0.8934375784638483 chr9 141213431 10826375 0.07666675133755514 0.6226042076988688 chr10 135534747 7085915 0.052281168902023334 0.882533101893162 chr11 135006516 11701912 0.08667664603684759 0.608341860486209 chr12 133851895 6237169 0.046597539765873316 0.31985138223002774 chr13 115169878 7078152 0.061458361534428296 0.34179827905539123 chr14 107349540 8121143 0.07565140008983737 0.9309730627042277 chr15 102531392 7415269 0.07232193824111936 0.37001824815789114 chr16 90354753 7239964 0.0801282031062605 0.43477586080163183 chr17 81195210 3539316 0.043590206860724914 0.34500858931143163 chr18 78077248 7015465 0.08985287237582965 1.0064044237727763 chr19 59128983 5840246 0.09877129122954813 1.2113441415089403 chr20 63025520 5457744 0.0865957789796895 0.4278974859601588 chr21 48129895 3361906 0.06985068220074031 0.40185580234268076 chr22 51304566 1531916 0.029859252683279693 0.2322751768069903 chrMT 16571 399067 24.082252127210186 13.218694256076882 chrX 155270560 15500168 0.09982683130659153 0.4991352651282001 chrY 59373566 652679 0.010992753913416621 0.22749450017959263