BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240019.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 = 1,879,110 number of mapped reads = 1,491,419 (79.37%) number of supplementary alignments = 10,269 (0.55%) number of secondary alignments = 0 number of mapped bases = 92,975,008 bp number of sequenced bases = 92,931,000 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 210,305 duplication rate = 11.25% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6035 >>>>>>> ACTG content number of A's = 25,356,649 bp (27.29%) number of C's = 16,384,298 bp (17.63%) number of T's = 30,154,222 bp (32.45%) number of G's = 20,974,381 bp (22.57%) number of N's = 61,450 bp (0.07%) GC percentage = 40.2% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 870,379 number of insertions = 6,512 mapped reads with insertion percentage = 0.43% number of deletions = 25,969 mapped reads with deletion percentage = 1.72% homopolymer indels = 48.54% >>>>>>> Coverage mean coverageData = 0.03X std coverageData = 0.3152X There is a 1.82% of reference with a coverageData >= 1X There is a 0.69% of reference with a coverageData >= 2X There is a 0.27% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% 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 6433168 0.025810038001871215 0.4135031489664944 chr2 243199373 9874359 0.04060190977548285 0.3991968706993607 chr3 198022430 6005719 0.03032847844559831 0.26144276132176614 chr4 191154276 5979371 0.03128034133016203 0.2719848722486462 chr5 180915260 5486595 0.03032687789852553 0.2635236633910901 chr6 171115067 5120210 0.029922613418957432 0.2852123211977677 chr7 159138663 4954696 0.031134457878410102 0.3737602786820204 chr8 146364022 5204530 0.03555880693139192 0.45496986314842797 chr9 141213431 3245191 0.022980753155130124 0.26734726197298925 chr10 135534747 5500138 0.040581017943686425 0.33479068650675353 chr11 135006516 4474276 0.03314118557062831 0.312176757691702 chr12 133851895 4612883 0.03446259016355353 0.2826116496230567 chr13 115169878 2341953 0.020334770173152394 0.21316428977628726 chr14 107349540 3303947 0.03077746770037394 0.2701755355362312 chr15 102531392 2367049 0.02308609055068715 0.2303427953239385 chr16 90354753 2705420 0.02994219905620239 0.25976093461532807 chr17 81195210 2544331 0.03133597412950838 0.27228111142914696 chr18 78077248 2115988 0.02710121135417068 0.3893879733384124 chr19 59128983 1596780 0.02700503068013194 0.3218242965305187 chr20 63025520 1910622 0.030315053330777754 0.2636084051769432 chr21 48129895 1316231 0.027347472916780725 0.2569029177884864 chr22 51304566 884365 0.017237549577945946 0.1903506894272215 chrMT 16571 23111 1.3946653792770503 1.9210762005263835 chrX 155270560 4769338 0.03071630578262872 0.2744235269072298 chrY 59373566 204737 0.0034482853867999104 0.08925480215757907