BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818854.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 895,951 number of mapped reads = 842,150 (94%) number of supplementary alignments = 13,013 (1.45%) number of secondary alignments = 0 number of mapped bases = 78,060,734 bp number of sequenced bases = 78,015,400 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 79,383 duplication rate = 7.32% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.2494 >>>>>>> ACTG content number of A's = 21,229,244 bp (27.21%) number of C's = 16,232,917 bp (20.81%) number of T's = 22,853,593 bp (29.29%) number of G's = 17,698,581 bp (22.69%) number of N's = 1,065 bp (0%) GC percentage = 43.49% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 467,125 number of insertions = 10,894 mapped reads with insertion percentage = 1.25% number of deletions = 22,691 mapped reads with deletion percentage = 2.63% homopolymer indels = 41.4% >>>>>>> Coverage mean coverageData = 0.0252X std coverageData = 0.3286X There is a 2.13% of reference with a coverageData >= 1X There is a 0.25% of reference with a coverageData >= 2X There is a 0.05% 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 7472687 0.029980615374274232 0.49076449614904405 chr2 243199373 5882830 0.024189330455222844 0.3795105226562804 chr3 198022430 4821499 0.02434824681224243 0.18101834537669748 chr4 191154276 3900686 0.02040595733259977 0.20862282517053907 chr5 180915260 3505436 0.01937612117407896 0.1585493504527483 chr6 171115067 3849766 0.02249811233747172 0.18310020160904628 chr7 159138663 6975681 0.043833980181170684 0.6823267465516802 chr8 146364022 6708281 0.04583285501678821 0.3047560777644206 chr9 141213431 2896472 0.020511306746735725 0.30280096400240114 chr10 135534747 3795663 0.02800509156519103 0.5339281671450281 chr11 135006516 3509127 0.025992278772677905 0.23208338046527846 chr12 133851895 3038397 0.02269969356802905 0.17038404464869544 chr13 115169878 2357880 0.020473061541317252 0.1607073626515173 chr14 107349540 2246502 0.020926983012689204 0.17365543561953822 chr15 102531392 1727577 0.01684924944742777 0.14476575156152233 chr16 90354753 2003497 0.0221736757998774 0.252512276524991 chr17 81195210 2019682 0.024874398378919152 0.25859651190283833 chr18 78077248 1502398 0.01924245588164173 0.3404071511713963 chr19 59128983 1458575 0.024667682851910372 0.4868186268752242 chr20 63025520 3313878 0.05257993904691306 0.272917979832232 chr21 48129895 762871 0.015850252737929307 0.17253196296278253 chr22 51304566 767731 0.014964184669255365 0.1419650321148086 chrMT 16571 95358 5.754510892523083 4.607715288584404 chrX 155270560 3150504 0.02029041435800837 0.199466032684445 chrY 59373566 297756 0.005014959013915385 0.33339818548259864