BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124892.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 = 4,740,286 number of mapped reads = 4,665,105 (98.41%) number of supplementary alignments = 22,791 (0.48%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,338,255 number of mapped paired reads (second in pair) = 2,326,850 number of mapped paired reads (both in pair) = 4,642,284 number of mapped paired reads (singletons) = 22,821 number of mapped bases = 403,414,315 bp number of sequenced bases = 403,194,342 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 430,828 duplication rate = 5.6% >>>>>>> Insert size mean insert size = 37,333.5266 std insert size = 1,829,252.9566 median insert size = 192 >>>>>>> Mapping quality mean mapping quality = 52.6102 >>>>>>> ACTG content number of A's = 114,712,455 bp (28.45%) number of C's = 74,169,458 bp (18.4%) number of T's = 121,281,354 bp (30.08%) number of G's = 92,877,384 bp (23.04%) number of N's = 153,691 bp (0.04%) GC percentage = 41.43% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 3,308,251 number of insertions = 55,922 mapped reads with insertion percentage = 1.17% number of deletions = 127,299 mapped reads with deletion percentage = 2.67% homopolymer indels = 47.06% >>>>>>> Coverage mean coverageData = 0.1303X std coverageData = 2.2375X There is a 9% of reference with a coverageData >= 1X There is a 2.33% of reference with a coverageData >= 2X There is a 0.61% of reference with a coverageData >= 3X There is a 0.22% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% 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 0.01% of reference with a coverageData >= 25X There is a 0.01% 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 40899846 0.16409125014777798 1.9643990472852677 chr2 243199373 32192687 0.13237158715865605 1.4641189729178983 chr3 198022430 25123317 0.12687106708063323 0.5573231625314576 chr4 191154276 17080334 0.08935365903088666 0.9887704957836856 chr5 180915260 21322745 0.1178604004991066 0.4505620927125654 chr6 171115067 28991276 0.16942561814267354 1.3663180246682842 chr7 159138663 22220748 0.139631360356471 1.6206687283243584 chr8 146364022 25613121 0.17499601780552326 0.7654265378330317 chr9 141213431 12330803 0.08732032720032133 1.6879191523577521 chr10 135534747 22852276 0.16860824626765267 9.05195292992118 chr11 135006516 21260190 0.15747528808165082 1.3983829369651837 chr12 133851895 17186867 0.12840211937231072 0.45543232027661085 chr13 115169878 19852319 0.17237422965751514 0.5397661428017008 chr14 107349540 7144461 0.06655325211454097 0.38304081951979563 chr15 102531392 13135235 0.12810939892438014 0.46525066279472627 chr16 90354753 14321729 0.1585055409315324 1.592156816577376 chr17 81195210 11903736 0.14660638232230694 1.6430813311365335 chr18 78077248 10143924 0.12992163863152553 1.9555939033151746 chr19 59128983 5676869 0.0960082300079472 1.225922115632911 chr20 63025520 7776315 0.1233835912817538 0.5074601794716529 chr21 48129895 6100224 0.12674500952059006 0.6226524097487743 chr22 51304566 4674688 0.09111641252359488 0.41018326735189314 chrMT 16571 196320 11.847202944903747 7.832825206575204 chrX 155270560 14333198 0.09231111164923989 0.6381454902426148 chrY 59373566 1081087 0.01820822080991396 1.2083964715702573