BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818935.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 = 2,505,383 number of mapped reads = 2,391,127 (95.44%) number of supplementary alignments = 29,145 (1.16%) number of secondary alignments = 0 number of mapped bases = 222,301,616 bp number of sequenced bases = 222,187,194 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,482,455 duplication rate = 48.92% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.132 >>>>>>> ACTG content number of A's = 66,091,805 bp (29.75%) number of C's = 44,101,777 bp (19.85%) number of T's = 64,171,111 bp (28.88%) number of G's = 47,812,359 bp (21.52%) number of N's = 10,142 bp (0%) GC percentage = 41.37% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 1,295,382 number of insertions = 27,528 mapped reads with insertion percentage = 1.13% number of deletions = 66,543 mapped reads with deletion percentage = 2.73% homopolymer indels = 44.38% >>>>>>> Coverage mean coverageData = 0.0718X std coverageData = 0.7775X There is a 2% of reference with a coverageData >= 1X There is a 1.27% of reference with a coverageData >= 2X There is a 0.92% of reference with a coverageData >= 3X There is a 0.69% of reference with a coverageData >= 4X There is a 0.52% of reference with a coverageData >= 5X There is a 0.4% of reference with a coverageData >= 6X There is a 0.3% of reference with a coverageData >= 7X There is a 0.23% of reference with a coverageData >= 8X There is a 0.18% of reference with a coverageData >= 9X There is a 0.14% of reference with a coverageData >= 10X There is a 0.1% of reference with a coverageData >= 11X There is a 0.08% of reference with a coverageData >= 12X There is a 0.06% of reference with a coverageData >= 13X There is a 0.05% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% 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 28850050 0.11574715394590732 1.0440298828755852 chr2 243199373 16414206 0.06749279736013135 0.8825352624892984 chr3 198022430 16954217 0.08561765957523094 0.7686861503896051 chr4 191154276 15272741 0.07989745936941531 0.7666036549738242 chr5 180915260 12998735 0.07184985390397693 0.7128349873461498 chr6 171115067 11156327 0.0651978063392863 0.6806647221521724 chr7 159138663 8386938 0.05270207655320065 0.6415684799462325 chr8 146364022 16213328 0.11077399881782424 0.9359855247447917 chr9 141213431 9694144 0.0686488808560993 0.8086665145979901 chr10 135534747 12513855 0.09232949687802199 0.9202216026024217 chr11 135006516 6611253 0.048969880831529644 0.5989064396149519 chr12 133851895 10132914 0.07570243215458398 0.7398822957122724 chr13 115169878 4177134 0.036269327297542155 0.4938801312620371 chr14 107349540 5852273 0.054516051023600104 0.625758353716239 chr15 102531392 6035207 0.05886204100301301 0.642173036520817 chr16 90354753 4438450 0.04912248501193955 0.6974303902411203 chr17 81195210 4308132 0.05305894276275657 0.6396259391732875 chr18 78077248 4900517 0.0627649811632705 0.8559288595135115 chr19 59128983 2028444 0.03430540992054607 0.6791245559219865 chr20 63025520 4192466 0.06652013343166387 0.7170598454172361 chr21 48129895 2348984 0.04880509296768672 0.5938651645540202 chr22 51304566 2047097 0.03990087354018354 0.5772283364820349 chrMT 16571 363249 21.92076519220325 19.753821090173368 chrX 155270560 15870966 0.10221490796452334 0.8636687741980758 chrY 59373566 539989 0.009094771232032787 0.4978849497249097