BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617672.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 = 30,059,447 (93.94%) number of supplementary alignments = 165,242 (0.52%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,276,011 number of mapped paired reads (second in pair) = 14,783,436 number of mapped paired reads (both in pair) = 29,208,448 number of mapped paired reads (singletons) = 850,999 number of mapped bases = 2,898,675,317 bp number of sequenced bases = 2,896,927,854 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,760,565 duplication rate = 10.44% >>>>>>> Insert size mean insert size = 45,696.306 std insert size = 1,996,448.9945 median insert size = 221 >>>>>>> Mapping quality mean mapping quality = 52.4936 >>>>>>> ACTG content number of A's = 862,009,200 bp (29.76%) number of C's = 574,789,429 bp (19.84%) number of T's = 860,749,390 bp (29.71%) number of G's = 596,291,666 bp (20.58%) number of N's = 3,088,169 bp (0.11%) GC percentage = 40.42% >>>>>>> Mismatches and indels general error rate = 0.0169 number of mismatches = 47,980,981 number of insertions = 453,176 mapped reads with insertion percentage = 1.48% number of deletions = 1,057,249 mapped reads with deletion percentage = 3.44% homopolymer indels = 47.43% >>>>>>> Coverage mean coverageData = 0.9364X std coverageData = 10.3228X There is a 33.11% of reference with a coverageData >= 1X There is a 19.1% of reference with a coverageData >= 2X There is a 11.62% of reference with a coverageData >= 3X There is a 7.4% of reference with a coverageData >= 4X There is a 4.85% of reference with a coverageData >= 5X There is a 3.28% of reference with a coverageData >= 6X There is a 2.27% of reference with a coverageData >= 7X There is a 1.61% of reference with a coverageData >= 8X There is a 1.16% of reference with a coverageData >= 9X There is a 0.86% of reference with a coverageData >= 10X There is a 0.64% of reference with a coverageData >= 11X There is a 0.49% of reference with a coverageData >= 12X There is a 0.38% of reference with a coverageData >= 13X There is a 0.3% of reference with a coverageData >= 14X There is a 0.24% 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 0.02% 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 177738490 0.7130914630700158 9.958953681610113 chr2 243199373 299195740 1.23024881318259 11.890750773776476 chr3 198022430 243133806 1.2278094254272105 2.4672138840197966 chr4 191154276 162084234 0.8479236635020396 8.067751437676066 chr5 180915260 192052635 1.0615612801263974 2.3157426870908755 chr6 171115067 140302698 0.8199318766009074 5.700563876880717 chr7 159138663 226581041 1.4237963090088297 13.105116504943775 chr8 146364022 128959555 0.881087805854365 4.064401161960159 chr9 141213431 118617652 0.8399884569053492 19.41397016029887 chr10 135534747 122591895 0.9045052852756644 21.105820011821088 chr11 135006516 159326793 1.180141505170017 11.868784548271814 chr12 133851895 123895789 0.9256184904965298 2.163964963604026 chr13 115169878 124542066 1.0813770767387632 2.3057203612884107 chr14 107349540 83047132 0.7736142325342056 2.4827812255672255 chr15 102531392 61955486 0.6042587035197962 1.6976549581882243 chr16 90354753 80356955 0.8893495066053692 16.577881815181318 chr17 81195210 71348747 0.8787309867170736 12.356324068906293 chr18 78077248 53475368 0.6849033408554563 17.993548369790805 chr19 59128983 30844522 0.5216481061411119 5.938871475792929 chr20 63025520 78566384 1.2465804962815064 3.0314104127306765 chr21 48129895 42261656 0.8780749677513321 4.308903905268884 chr22 51304566 18638238 0.36328614494078365 1.2679607809121558 chrMT 16571 3100049 187.07676060587775 131.0265420597877 chrX 155270560 144418414 0.9301081544370033 4.262289451516096 chrY 59373566 11639972 0.19604636851355703 16.42172773382553