BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818892.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 = 1,408,266 number of mapped reads = 1,385,999 (98.42%) number of supplementary alignments = 19,557 (1.39%) number of secondary alignments = 0 number of mapped bases = 128,323,520 bp number of sequenced bases = 128,242,823 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 237,557 duplication rate = 14.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.1738 >>>>>>> ACTG content number of A's = 37,746,527 bp (29.43%) number of C's = 28,362,980 bp (22.12%) number of T's = 35,578,655 bp (27.74%) number of G's = 26,552,669 bp (20.7%) number of N's = 1,992 bp (0%) GC percentage = 42.82% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 787,052 number of insertions = 17,494 mapped reads with insertion percentage = 1.22% number of deletions = 40,967 mapped reads with deletion percentage = 2.89% homopolymer indels = 40.82% >>>>>>> Coverage mean coverageData = 0.0415X std coverageData = 0.5571X There is a 3.11% of reference with a coverageData >= 1X There is a 0.64% of reference with a coverageData >= 2X There is a 0.17% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 12181184 0.048871228288735136 0.8249613515358275 chr2 243199373 9741071 0.04005384915198774 0.763680575395149 chr3 198022430 8088137 0.040844549781557576 0.25257072191037694 chr4 191154276 6463489 0.033812944890649475 0.31514710695100284 chr5 180915260 5660065 0.03128572459835616 0.2342205937205241 chr6 171115067 6319021 0.03692848976297335 0.26832323717649115 chr7 159138663 11503601 0.07228665104469302 1.2766437846956864 chr8 146364022 11110814 0.07591219377669192 0.4561370824382501 chr9 141213431 4698546 0.033272656621451256 0.46524054402029424 chr10 135534747 6041371 0.04457433339953776 0.8349433140972495 chr11 135006516 5626140 0.04167309968949943 0.3254533884513089 chr12 133851895 5005919 0.037398940074774435 0.24383353536388905 chr13 115169878 3866103 0.033568699273954256 0.22585577926781625 chr14 107349540 3738032 0.034821127319222794 0.25819254894597166 chr15 102531392 3541345 0.034539129245411984 0.23144514805986774 chr16 90354753 3273174 0.036225808729730025 0.5455462124799704 chr17 81195210 3207463 0.039503106156139015 0.35865106187212925 chr18 78077248 2468898 0.03162122210045108 0.5273730164305717 chr19 59128983 2286729 0.03867357231562735 0.7115415652959011 chr20 63025520 5271410 0.08363929405104471 0.3919366983563962 chr21 48129895 1236854 0.025698248458676257 0.2712202768996509 chr22 51304566 1172836 0.022860265497616723 0.20988937768862528 chrMT 16571 151941 9.169090579928792 6.318696027352107 chrX 155270560 5182892 0.03337974693979335 0.28635209860586247 chrY 59373566 486485 0.008193629468036331 0.578702475443353