BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004010.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 = 2,314,613 number of mapped reads = 2,089,995 (90.3%) number of supplementary alignments = 19,670 (0.85%) number of secondary alignments = 0 number of mapped bases = 141,101,991 bp number of sequenced bases = 141,045,473 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 120,293 duplication rate = 4.68% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.8962 >>>>>>> ACTG content number of A's = 39,996,235 bp (28.36%) number of C's = 26,223,957 bp (18.59%) number of T's = 44,765,445 bp (31.74%) number of G's = 30,035,316 bp (21.29%) number of N's = 24,520 bp (0.02%) GC percentage = 39.89% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,196,284 number of insertions = 10,071 mapped reads with insertion percentage = 0.48% number of deletions = 32,727 mapped reads with deletion percentage = 1.55% homopolymer indels = 47.03% >>>>>>> Coverage mean coverageData = 0.0456X std coverageData = 0.3961X There is a 3.52% of reference with a coverageData >= 1X There is a 0.75% of reference with a coverageData >= 2X There is a 0.17% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 11956931 0.04797151939693663 0.7132201945844879 chr2 243199373 11130732 0.04576793049544581 0.38746717127639374 chr3 198022430 9665591 0.048810586760297814 0.27260208538630537 chr4 191154276 9699345 0.05074092614072625 0.29734131707742434 chr5 180915260 8523602 0.047113781336079665 0.26944954795700815 chr6 171115067 8340455 0.048741791977909225 0.29014901392280473 chr7 159138663 7751571 0.048709539554193694 0.4954391352308871 chr8 146364022 10745820 0.07341845252107106 0.6865371261632021 chr9 141213431 5409167 0.03830490458092474 0.33591474354783174 chr10 135534747 6908389 0.05097134980448962 0.3755804209538549 chr11 135006516 5146954 0.03812374507908937 0.29140445529816267 chr12 133851895 6409238 0.04788305761379023 0.27594180375655797 chr13 115169878 4729192 0.04106275080017016 0.25597859051398886 chr14 107349540 3472397 0.03234664070288517 0.2432536566864754 chr15 102531392 4850319 0.047305697361448094 0.2679673544620556 chr16 90354753 3775908 0.041789810437531716 0.27067464855976525 chr17 81195210 2989820 0.03682261552128506 0.24996941945600035 chr18 78077248 3787798 0.04851346707301979 0.5872051029844568 chr19 59128983 1947005 0.03292809889863994 0.4914693939740273 chr20 63025520 2710416 0.04300505572980596 0.26606147842704414 chr21 48129895 1863420 0.03871647756555463 0.25983051546679437 chr22 51304566 1135731 0.02213703552233538 0.1775873695437432 chrMT 16571 31980 1.9298774968318146 2.105217830249159 chrX 155270560 7781178 0.05011367254681119 0.2947517119658175 chrY 59373566 339032 0.005710150540730533 0.12649448311793943