BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238641.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 = 15,238,711 number of mapped reads = 13,618,052 (89.36%) number of supplementary alignments = 106,875 (0.7%) number of secondary alignments = 0 number of mapped bases = 858,423,248 bp number of sequenced bases = 858,070,045 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,554,346 duplication rate = 18.62% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.4738 >>>>>>> ACTG content number of A's = 215,223,652 bp (25.08%) number of C's = 155,726,876 bp (18.15%) number of T's = 281,641,788 bp (32.82%) number of G's = 205,431,378 bp (23.94%) number of N's = 46,351 bp (0.01%) GC percentage = 42.09% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 4,444,278 number of insertions = 53,706 mapped reads with insertion percentage = 0.39% number of deletions = 203,336 mapped reads with deletion percentage = 1.48% homopolymer indels = 43.02% >>>>>>> Coverage mean coverageData = 0.2773X std coverageData = 2.7157X There is a 9.01% of reference with a coverageData >= 1X There is a 5.25% of reference with a coverageData >= 2X There is a 3.52% of reference with a coverageData >= 3X There is a 2.45% of reference with a coverageData >= 4X There is a 1.75% of reference with a coverageData >= 5X There is a 1.27% of reference with a coverageData >= 6X There is a 0.93% of reference with a coverageData >= 7X There is a 0.69% of reference with a coverageData >= 8X There is a 0.52% of reference with a coverageData >= 9X There is a 0.39% of reference with a coverageData >= 10X There is a 0.3% of reference with a coverageData >= 11X There is a 0.23% of reference with a coverageData >= 12X There is a 0.18% of reference with a coverageData >= 13X There is a 0.14% of reference with a coverageData >= 14X There is a 0.11% of reference with a coverageData >= 15X There is a 0.09% of reference with a coverageData >= 16X There is a 0.07% of reference with a coverageData >= 17X There is a 0.06% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% 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 57134042 0.2292232684146452 3.8053136132279306 chr2 243199373 81379829 0.3346218700983246 6.106847472025721 chr3 198022430 113697237 0.5741634268400807 1.9009174774974584 chr4 191154276 29127403 0.15237641348917563 1.1797859265914128 chr5 180915260 23615358 0.13053270354308422 0.9458669859488725 chr6 171115067 136207724 0.7960007636265017 3.9942660660283416 chr7 159138663 17838511 0.11209413641988433 1.6824895086605345 chr8 146364022 12381648 0.08459488766986739 1.1722017978253758 chr9 141213431 54597169 0.3866287265550541 1.7296356025306445 chr10 135534747 35220788 0.25986537607215954 2.3802352821359833 chr11 135006516 113708683 0.8422458883391969 2.8767378083380506 chr12 133851895 15068048 0.11257254146457919 0.9089731349818025 chr13 115169878 10828742 0.0940240815397929 1.3791273617142483 chr14 107349540 8976143 0.08361603598860322 0.810139656258847 chr15 102531392 9483192 0.09249061984840701 1.2325416314595334 chr16 90354753 7365467 0.08151720585191573 0.9490361781202259 chr17 81195210 7281330 0.08967684177428693 1.0633043957105301 chr18 78077248 6809962 0.08722082520121612 3.784072428023021 chr19 59128983 9704020 0.16411613235424666 2.420759511818941 chr20 63025520 4701628 0.07459879743951339 0.7477771175979896 chr21 48129895 4298910 0.08931891499036099 1.0206018283499534 chr22 51304566 2975367 0.05799419490265252 0.565406747612071 chrMT 16571 303106 18.2913523625611 12.524949184536483 chrX 155270560 92902247 0.5983249303667095 2.206773655547649 chrY 59373566 2816694 0.04744020259790359 1.1827479505965575