BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124885.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 6,369,188 number of mapped reads = 6,149,661 (96.55%) number of supplementary alignments = 6,174 (0.1%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,095,351 number of mapped paired reads (second in pair) = 3,054,310 number of mapped paired reads (both in pair) = 6,045,404 number of mapped paired reads (singletons) = 104,257 number of mapped bases = 411,160,044 bp number of sequenced bases = 410,991,101 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 351,072 duplication rate = 3.43% >>>>>>> Insert size mean insert size = 79,839.6272 std insert size = 2,733,938.4445 median insert size = 215 >>>>>>> Mapping quality mean mapping quality = 51.9521 >>>>>>> ACTG content number of A's = 118,161,699 bp (28.75%) number of C's = 76,114,329 bp (18.52%) number of T's = 122,558,035 bp (29.82%) number of G's = 94,153,307 bp (22.91%) number of N's = 3,731 bp (0%) GC percentage = 41.43% >>>>>>> Mismatches and indels general error rate = 0.0073 number of mismatches = 2,940,156 number of insertions = 45,042 mapped reads with insertion percentage = 0.73% number of deletions = 116,120 mapped reads with deletion percentage = 1.87% homopolymer indels = 49.78% >>>>>>> Coverage mean coverageData = 0.1328X std coverageData = 1.2263X There is a 9.95% of reference with a coverageData >= 1X There is a 2.06% of reference with a coverageData >= 2X There is a 0.5% of reference with a coverageData >= 3X There is a 0.15% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% 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% 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 35247554 0.1414141070485036 1.764942173321576 chr2 243199373 37520504 0.15427878590788965 1.3043109767270418 chr3 198022430 26792577 0.13530071820651832 0.4541327025510813 chr4 191154276 19504715 0.10203650898188645 0.5364473483529856 chr5 180915260 22665402 0.1252818695338359 0.43143865488004013 chr6 171115067 33182366 0.19391843501425857 1.283741039360798 chr7 159138663 21871202 0.13743487338460297 1.8179731399895 chr8 146364022 24241974 0.1656279573951582 0.6424170103090212 chr9 141213431 15656856 0.11087370294118837 1.1906051380283131 chr10 135534747 15088785 0.11132779847222499 2.471461566286424 chr11 135006516 28636085 0.21210891035807486 1.1305629547005611 chr12 133851895 13307059 0.09941629141671846 0.3930466153188925 chr13 115169878 15209857 0.13206454034795453 0.4881189660592587 chr14 107349540 6843187 0.06374677525399736 0.3975838343103204 chr15 102531392 8970626 0.08749150699134174 0.35627391834827743 chr16 90354753 12887454 0.14263172187521778 2.072907759586987 chr17 81195210 9861488 0.12145406114473994 1.7927128146214653 chr18 78077248 12103418 0.15501850167669845 1.8326026162010445 chr19 59128983 5699949 0.09639856312089792 1.317718889667067 chr20 63025520 10865434 0.17239737173132408 0.5348075291323494 chr21 48129895 3600104 0.07479974764125291 0.41425668306318886 chr22 51304566 2912229 0.05676354420384338 0.28193055943607387 chrMT 16571 109503 6.608110554583308 4.237346059072962 chrX 155270560 27653037 0.17809581545915723 0.8842518673518059 chrY 59373566 728679 0.012272784828184313 0.5310484754626876