BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617652.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 30,117,505 (94.12%) number of supplementary alignments = 143,278 (0.45%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,129,692 number of mapped paired reads (second in pair) = 14,987,813 number of mapped paired reads (both in pair) = 29,497,622 number of mapped paired reads (singletons) = 619,883 number of mapped bases = 2,924,008,390 bp number of sequenced bases = 2,922,250,972 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,849,160 duplication rate = 10.59% >>>>>>> Insert size mean insert size = 34,294.8193 std insert size = 1,696,186.6562 median insert size = 221 >>>>>>> Mapping quality mean mapping quality = 52.6244 >>>>>>> ACTG content number of A's = 872,114,601 bp (29.84%) number of C's = 581,489,981 bp (19.9%) number of T's = 869,362,927 bp (29.75%) number of G's = 597,421,580 bp (20.44%) number of N's = 1,861,883 bp (0.06%) GC percentage = 40.34% >>>>>>> Mismatches and indels general error rate = 0.0155 number of mismatches = 44,480,315 number of insertions = 453,178 mapped reads with insertion percentage = 1.48% number of deletions = 1,065,640 mapped reads with deletion percentage = 3.46% homopolymer indels = 47.64% >>>>>>> Coverage mean coverageData = 0.9445X std coverageData = 10.6784X There is a 33.23% of reference with a coverageData >= 1X There is a 19.23% of reference with a coverageData >= 2X There is a 11.74% of reference with a coverageData >= 3X There is a 7.48% of reference with a coverageData >= 4X There is a 4.92% of reference with a coverageData >= 5X There is a 3.33% of reference with a coverageData >= 6X There is a 2.3% of reference with a coverageData >= 7X There is a 1.63% of reference with a coverageData >= 8X There is a 1.18% of reference with a coverageData >= 9X There is a 0.87% of reference with a coverageData >= 10X There is a 0.66% of reference with a coverageData >= 11X There is a 0.5% of reference with a coverageData >= 12X There is a 0.39% of reference with a coverageData >= 13X There is a 0.31% of reference with a coverageData >= 14X There is a 0.25% of reference with a coverageData >= 15X There is a 0.2% of reference with a coverageData >= 16X There is a 0.16% of reference with a coverageData >= 17X There is a 0.14% of reference with a coverageData >= 18X There is a 0.12% of reference with a coverageData >= 19X There is a 0.1% of reference with a coverageData >= 20X There is a 0.09% of reference with a coverageData >= 21X There is a 0.07% of reference with a coverageData >= 22X There is a 0.07% of reference with a coverageData >= 23X There is a 0.06% of reference with a coverageData >= 24X There is a 0.05% of reference with a coverageData >= 25X There is a 0.05% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.04% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.03% of reference with a coverageData >= 33X There is a 0.03% of reference with a coverageData >= 34X There is a 0.03% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 179011925 0.7182005175425421 10.283875013831768 chr2 243199373 301947057 1.2415618234344707 12.137785881263039 chr3 198022430 244909341 1.2367757581805252 2.4652191296554142 chr4 191154276 164010703 0.8580017482841974 8.32599030148644 chr5 180915260 193840942 1.0714460571208864 2.327391805653888 chr6 171115067 142112397 0.8305077950850465 5.787715631192377 chr7 159138663 229145438 1.439910538899023 13.314664693757834 chr8 146364022 130240813 0.8898417194356684 4.156952433517527 chr9 141213431 119909853 0.8491391516434439 20.591796708836846 chr10 135534747 124031344 0.9151258016514392 21.785782246326537 chr11 135006516 160681029 1.1901723987899961 12.213163740847103 chr12 133851895 124684883 0.9315137675114723 2.1377542578103435 chr13 115169878 125772560 1.0920612419160503 2.2769866374065297 chr14 107349540 83476200 0.7776111569737514 2.446918390796369 chr15 102531392 62289772 0.6075190318297834 1.5659334425571683 chr16 90354753 81309870 0.899895880408195 17.08874965966445 chr17 81195210 71459793 0.8800986289708469 12.764520873763143 chr18 78077248 53963909 0.6911604901853098 18.488018154272602 chr19 59128983 30694195 0.5191057488676915 6.2281291999049175 chr20 63025520 78472436 1.2450898620114519 3.0229879784157476 chr21 48129895 42651662 0.886178164319702 4.357385656950097 chr22 51304566 18772552 0.36590411855350263 1.2606592111836241 chrMT 16571 3054753 184.3433106028604 129.72074311413172 chrX 155270560 145798449 0.9389960917253084 4.393686573516404 chrY 59373566 11766514 0.1981776536716693 17.53525558425329