BamQC report ----------------------------------- >>>>>>> Input bam file = SRR927039.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 32,375,858 number of mapped reads = 31,594,902 (97.59%) number of supplementary alignments = 637,274 (1.97%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,879,791 number of mapped paired reads (second in pair) = 15,715,111 number of mapped paired reads (both in pair) = 31,142,772 number of mapped paired reads (singletons) = 452,130 number of mapped bases = 2,885,644,321 bp number of sequenced bases = 2,883,462,065 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,985,492 duplication rate = 7.19% >>>>>>> Insert size mean insert size = 233,013.8771 std insert size = 4,713,082.3343 median insert size = 184 >>>>>>> Mapping quality mean mapping quality = 52.6449 >>>>>>> ACTG content number of A's = 824,299,562 bp (28.59%) number of C's = 564,124,415 bp (19.56%) number of T's = 838,148,611 bp (29.07%) number of G's = 656,498,277 bp (22.77%) number of N's = 391,200 bp (0.01%) GC percentage = 42.33% >>>>>>> Mismatches and indels general error rate = 0.011 number of mismatches = 30,927,659 number of insertions = 495,004 mapped reads with insertion percentage = 1.53% number of deletions = 1,481,945 mapped reads with deletion percentage = 4.57% homopolymer indels = 51.58% >>>>>>> Coverage mean coverageData = 0.9321X std coverageData = 3.7192X There is a 35.94% of reference with a coverageData >= 1X There is a 20.2% of reference with a coverageData >= 2X There is a 11.82% of reference with a coverageData >= 3X There is a 7.4% of reference with a coverageData >= 4X There is a 4.81% of reference with a coverageData >= 5X There is a 3.23% of reference with a coverageData >= 6X There is a 2.22% of reference with a coverageData >= 7X There is a 1.56% of reference with a coverageData >= 8X There is a 1.11% of reference with a coverageData >= 9X There is a 0.81% of reference with a coverageData >= 10X There is a 0.6% of reference with a coverageData >= 11X There is a 0.45% of reference with a coverageData >= 12X There is a 0.34% of reference with a coverageData >= 13X There is a 0.26% of reference with a coverageData >= 14X There is a 0.2% of reference with a coverageData >= 15X There is a 0.16% of reference with a coverageData >= 16X There is a 0.12% of reference with a coverageData >= 17X There is a 0.1% of reference with a coverageData >= 18X There is a 0.08% of reference with a coverageData >= 19X There is a 0.07% of reference with a coverageData >= 20X There is a 0.06% of reference with a coverageData >= 21X There is a 0.05% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% 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 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 232306032 0.9320178664670208 4.936642261746599 chr2 243199373 251583235 1.0344732056525492 7.020129991135328 chr3 198022430 192336541 0.9712866416193358 1.9375742230933062 chr4 191154276 178411713 0.9333388545281613 3.264909724412329 chr5 180915260 175475625 0.9699326911394871 1.9459061047774895 chr6 171115067 164605528 0.9619581190942116 1.959561955082343 chr7 159138663 148650734 0.9340956571942546 2.7504814990931767 chr8 146364022 147508888 1.0078220452291207 2.4137303920547177 chr9 141213431 122161096 0.8650812825304132 4.982411574487469 chr10 135534747 139144965 1.0266368446461924 5.331830712746022 chr11 135006516 136444924 1.01065435982364 3.003783710694876 chr12 133851895 129489450 0.9674084180877678 2.007155832009002 chr13 115169878 87147312 0.7566849380529864 1.6929445688193938 chr14 107349540 85907119 0.8002560513999408 1.8473553719326197 chr15 102531392 84942212 0.8284507831513689 1.8606547594579077 chr16 90354753 89865479 0.9945849666591419 5.482818406326335 chr17 81195210 72111074 0.8881198041115972 2.640449768505001 chr18 78077248 78330532 1.003244018026865 4.990337580198298 chr19 59128983 48400455 0.8185572040026462 3.046658528263551 chr20 63025520 66752998 1.0591423601106345 2.295852001403519 chr21 48129895 37579166 0.7807863698850787 2.9868719775709986 chr22 51304566 34440541 0.6712958257945306 1.8388457357715384 chrMT 16571 12351 0.7453382415062458 1.162242524067009 chrX 155270560 176128105 1.1343303263670848 2.4353445111154493 chrY 59373566 5908246 0.09950970436911268 3.470384616924619