BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238485.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 = 3,501,836 number of mapped reads = 2,875,739 (82.12%) number of supplementary alignments = 25,052 (0.72%) number of secondary alignments = 0 number of mapped bases = 175,643,879 bp number of sequenced bases = 175,565,270 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,217,199 duplication rate = 22.18% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 35.9639 >>>>>>> ACTG content number of A's = 43,619,919 bp (24.85%) number of C's = 29,836,289 bp (16.99%) number of T's = 60,571,021 bp (34.5%) number of G's = 41,534,130 bp (23.66%) number of N's = 3,911 bp (0%) GC percentage = 40.65% >>>>>>> Mismatches and indels general error rate = 0.0058 number of mismatches = 994,466 number of insertions = 10,617 mapped reads with insertion percentage = 0.37% number of deletions = 47,395 mapped reads with deletion percentage = 1.64% homopolymer indels = 41.36% >>>>>>> Coverage mean coverageData = 0.0567X std coverageData = 1.1522X There is a 1.5% of reference with a coverageData >= 1X There is a 0.84% of reference with a coverageData >= 2X There is a 0.64% of reference with a coverageData >= 3X There is a 0.51% of reference with a coverageData >= 4X There is a 0.4% of reference with a coverageData >= 5X There is a 0.32% of reference with a coverageData >= 6X There is a 0.26% of reference with a coverageData >= 7X There is a 0.21% of reference with a coverageData >= 8X There is a 0.17% of reference with a coverageData >= 9X There is a 0.13% of reference with a coverageData >= 10X There is a 0.11% of reference with a coverageData >= 11X There is a 0.09% of reference with a coverageData >= 12X There is a 0.07% of reference with a coverageData >= 13X There is a 0.06% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% 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 0.01% 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% 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 26159386 0.10495213971803906 1.3197113025386018 chr2 243199373 6913926 0.028429045333106185 2.364555382694922 chr3 198022430 4453807 0.022491426855028494 0.4399031462423767 chr4 191154276 12768173 0.06679512102569968 0.7459781068792599 chr5 180915260 6833185 0.037770086392933354 0.5519330971911174 chr6 171115067 14272391 0.08340814897381305 1.113960591934546 chr7 159138663 17777682 0.11171189744128993 1.112162722340083 chr8 146364022 11245617 0.07683320563574018 1.3112115186788031 chr9 141213431 2543995 0.018015248138826115 0.5211525443405116 chr10 135534747 7523391 0.05550894635159499 0.6932353144229131 chr11 135006516 14333142 0.10616629792890886 1.0967672219097044 chr12 133851895 1450329 0.010835326612297868 0.3270703718631827 chr13 115169878 946398 0.008217409069409624 0.62399238655775 chr14 107349540 919644 0.00856681826489429 0.3632996706183946 chr15 102531392 937872 0.009147169288406812 0.5260694574435167 chr16 90354753 8009199 0.08864170100714015 0.917722417198841 chr17 81195210 1827308 0.022505120683843294 0.4496419284680957 chr18 78077248 25094815 0.3214100860727058 3.3213289040246305 chr19 59128983 1491383 0.02522253765129023 0.6826918096209093 chr20 63025520 804897 0.012770969600885482 0.2864606226024135 chr21 48129895 1975729 0.04104993372622151 0.590535210885701 chr22 51304566 370474 0.007221072681912951 0.22922719457434274 chrMT 16571 29571 1.7845030474926076 3.842330312616111 chrX 155270560 6710748 0.04321970629847667 0.6384788720301741 chrY 59373566 250817 0.004224388341438006 0.38072830547663133