BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472571.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 379,444,244 number of mapped reads = 373,340,748 (98.39%) number of supplementary alignments = 464,813 (0.12%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 187,314,699 number of mapped paired reads (second in pair) = 186,026,049 number of mapped paired reads (both in pair) = 371,412,074 number of mapped paired reads (singletons) = 1,928,674 number of mapped bases = 34,640,212,338 bp number of sequenced bases = 34,633,701,479 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 253,744,245 duplication rate = 56.23% >>>>>>> Insert size mean insert size = 12,846.543 std insert size = 1,043,435.8203 median insert size = 140 >>>>>>> Mapping quality mean mapping quality = 51.8118 >>>>>>> ACTG content number of A's = 8,855,094,441 bp (25.57%) number of C's = 8,488,161,056 bp (24.51%) number of T's = 8,996,747,342 bp (25.98%) number of G's = 8,286,770,050 bp (23.93%) number of N's = 6,928,590 bp (0.02%) GC percentage = 48.44% >>>>>>> Mismatches and indels general error rate = 0.0097 number of mismatches = 329,730,002 number of insertions = 2,635,050 mapped reads with insertion percentage = 0.69% number of deletions = 2,838,387 mapped reads with deletion percentage = 0.74% homopolymer indels = 39.92% >>>>>>> Coverage mean coverageData = 11.1898X std coverageData = 118.5432X There is a 76.3% of reference with a coverageData >= 1X There is a 67.07% of reference with a coverageData >= 2X There is a 56.1% of reference with a coverageData >= 3X There is a 48.41% of reference with a coverageData >= 4X There is a 40.17% of reference with a coverageData >= 5X There is a 34.4% of reference with a coverageData >= 6X There is a 28.58% of reference with a coverageData >= 7X There is a 24.43% of reference with a coverageData >= 8X There is a 20.46% of reference with a coverageData >= 9X There is a 17.58% of reference with a coverageData >= 10X There is a 14.94% of reference with a coverageData >= 11X There is a 12.99% of reference with a coverageData >= 12X There is a 11.26% of reference with a coverageData >= 13X There is a 9.97% of reference with a coverageData >= 14X There is a 8.84% of reference with a coverageData >= 15X There is a 7.98% of reference with a coverageData >= 16X There is a 7.24% of reference with a coverageData >= 17X There is a 6.67% of reference with a coverageData >= 18X There is a 6.18% of reference with a coverageData >= 19X There is a 5.8% of reference with a coverageData >= 20X There is a 5.46% of reference with a coverageData >= 21X There is a 5.2% of reference with a coverageData >= 22X There is a 4.97% of reference with a coverageData >= 23X There is a 4.77% of reference with a coverageData >= 24X There is a 4.61% of reference with a coverageData >= 25X There is a 4.46% of reference with a coverageData >= 26X There is a 4.34% of reference with a coverageData >= 27X There is a 4.23% of reference with a coverageData >= 28X There is a 4.13% of reference with a coverageData >= 29X There is a 4.04% of reference with a coverageData >= 30X There is a 3.96% of reference with a coverageData >= 31X There is a 3.89% of reference with a coverageData >= 32X There is a 3.82% of reference with a coverageData >= 33X There is a 3.76% of reference with a coverageData >= 34X There is a 3.7% of reference with a coverageData >= 35X There is a 3.64% of reference with a coverageData >= 36X There is a 3.59% of reference with a coverageData >= 37X There is a 3.54% of reference with a coverageData >= 38X There is a 3.49% of reference with a coverageData >= 39X There is a 3.45% of reference with a coverageData >= 40X There is a 3.41% of reference with a coverageData >= 41X There is a 3.37% of reference with a coverageData >= 42X There is a 3.33% of reference with a coverageData >= 43X There is a 3.29% of reference with a coverageData >= 44X There is a 3.25% of reference with a coverageData >= 45X There is a 3.22% of reference with a coverageData >= 46X There is a 3.18% of reference with a coverageData >= 47X There is a 3.15% of reference with a coverageData >= 48X There is a 3.12% of reference with a coverageData >= 49X There is a 3.09% of reference with a coverageData >= 50X There is a 3.05% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2651555171 10.638108584692352 84.1741767334223 chr2 243199373 2718648557 11.178682426126157 84.01598174719695 chr3 198022430 1543359191 7.793860478330662 38.15574013804141 chr4 191154276 1286411411 6.729702510029124 47.660887449203706 chr5 180915260 1427415973 7.889969994792037 51.307871457498656 chr6 171115067 1831055351 10.700725442254598 47.47000453559584 chr7 159138663 3153678215 19.81717173908895 416.22758401670353 chr8 146364022 1750054492 11.95686254098702 177.73379528572943 chr9 141213431 1214967677 8.603768553714978 47.27164610370262 chr10 135534747 1592524731 11.749936944214017 71.15750569583125 chr11 135006516 1641702269 12.160170617246356 51.230297511600924 chr12 133851895 1614890610 12.064757170602627 50.11763769107467 chr13 115169878 1122985045 9.750683637956099 41.56906587630666 chr14 107349540 740838378 6.901178877897381 31.040144379959553 chr15 102531392 1306732923 12.744710644326373 63.246185436636296 chr16 90354753 1550309211 17.158026108488173 82.93279341312133 chr17 81195210 1524126148 18.771133765156836 103.59560843515892 chr18 78077248 531510202 6.807491498675773 52.408742322120645 chr19 59128983 1382793327 23.38604956219186 90.00735437474366 chr20 63025520 1278298588 20.282237861742356 90.45565907512726 chr21 48129895 487904682 10.137248003553717 66.59340329605632 chr22 51304566 586871224 11.43896673836009 57.96073237715012 chrMT 16571 16441115 992.1619093597249 236.85266634909783 chrX 155270560 1550446046 9.985447634116861 43.665215392434135 chrY 59373566 134691801 2.268548279549185 80.39760408107001