BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504613.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 479,878,740 number of mapped reads = 318,951,734 (66.47%) number of supplementary alignments = 2,056,872 (0.43%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 159,756,071 number of mapped paired reads (second in pair) = 159,195,663 number of mapped paired reads (both in pair) = 316,820,240 number of mapped paired reads (singletons) = 2,131,494 number of mapped bases = 31,679,878,708 bp number of sequenced bases = 31,671,786,777 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 87,866,397 duplication rate = 23.93% >>>>>>> Insert size mean insert size = 25,631.8194 std insert size = 1,547,673.6007 median insert size = 207 >>>>>>> Mapping quality mean mapping quality = 53.7564 >>>>>>> ACTG content number of A's = 8,187,809,421 bp (25.85%) number of C's = 7,579,442,928 bp (23.93%) number of T's = 8,226,662,777 bp (25.97%) number of G's = 7,676,058,059 bp (24.24%) number of N's = 1,813,592 bp (0.01%) GC percentage = 48.17% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 154,216,235 number of insertions = 2,354,731 mapped reads with insertion percentage = 0.72% number of deletions = 3,119,200 mapped reads with deletion percentage = 0.95% homopolymer indels = 40.14% >>>>>>> Coverage mean coverageData = 10.2335X std coverageData = 26.4255X There is a 68.94% of reference with a coverageData >= 1X There is a 59.39% of reference with a coverageData >= 2X There is a 52.1% of reference with a coverageData >= 3X There is a 46.44% of reference with a coverageData >= 4X There is a 41.76% of reference with a coverageData >= 5X There is a 37.83% of reference with a coverageData >= 6X There is a 34.46% of reference with a coverageData >= 7X There is a 31.56% of reference with a coverageData >= 8X There is a 29.02% of reference with a coverageData >= 9X There is a 26.78% of reference with a coverageData >= 10X There is a 24.8% of reference with a coverageData >= 11X There is a 23.03% of reference with a coverageData >= 12X There is a 21.45% of reference with a coverageData >= 13X There is a 20.03% of reference with a coverageData >= 14X There is a 18.74% of reference with a coverageData >= 15X There is a 17.57% of reference with a coverageData >= 16X There is a 16.51% of reference with a coverageData >= 17X There is a 15.54% of reference with a coverageData >= 18X There is a 14.65% of reference with a coverageData >= 19X There is a 13.84% of reference with a coverageData >= 20X There is a 13.09% of reference with a coverageData >= 21X There is a 12.4% of reference with a coverageData >= 22X There is a 11.76% of reference with a coverageData >= 23X There is a 11.16% of reference with a coverageData >= 24X There is a 10.61% of reference with a coverageData >= 25X There is a 10.1% of reference with a coverageData >= 26X There is a 9.63% of reference with a coverageData >= 27X There is a 9.18% of reference with a coverageData >= 28X There is a 8.77% of reference with a coverageData >= 29X There is a 8.38% of reference with a coverageData >= 30X There is a 8.01% of reference with a coverageData >= 31X There is a 7.67% of reference with a coverageData >= 32X There is a 7.35% of reference with a coverageData >= 33X There is a 7.05% of reference with a coverageData >= 34X There is a 6.76% of reference with a coverageData >= 35X There is a 6.49% of reference with a coverageData >= 36X There is a 6.24% of reference with a coverageData >= 37X There is a 6% of reference with a coverageData >= 38X There is a 5.78% of reference with a coverageData >= 39X There is a 5.56% of reference with a coverageData >= 40X There is a 5.36% of reference with a coverageData >= 41X There is a 5.17% of reference with a coverageData >= 42X There is a 4.98% of reference with a coverageData >= 43X There is a 4.81% of reference with a coverageData >= 44X There is a 4.65% of reference with a coverageData >= 45X There is a 4.49% of reference with a coverageData >= 46X There is a 4.34% of reference with a coverageData >= 47X There is a 4.2% of reference with a coverageData >= 48X There is a 4.06% of reference with a coverageData >= 49X There is a 3.93% of reference with a coverageData >= 50X There is a 3.81% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3213048875 12.890835987124783 25.764257363539805 chr2 243199373 1415504552 5.820346222685369 15.60381989125999 chr3 198022430 1788645042 9.032537586777417 24.55797075807299 chr4 191154276 1066126069 5.577306934007587 10.601886951338395 chr5 180915260 1544645870 8.537952354046862 24.478216877814976 chr6 171115067 1342114686 7.843346056721002 15.248940630336877 chr7 159138663 2533651741 15.921031968202472 29.499399023384214 chr8 146364022 2852073852 19.486167522780974 46.75895128450092 chr9 141213431 966745075 6.845985315660236 19.08205717723021 chr10 135534747 1557321168 11.490198657322908 23.78930587489653 chr11 135006516 1787565673 13.240588128353746 30.481483067942495 chr12 133851895 955365941 7.137485360218471 17.818978196520316 chr13 115169878 865112390 7.511620269320768 16.793487962175135 chr14 107349540 1122502769 10.456521462504636 20.95544873373321 chr15 102531392 966659714 9.427939045243821 19.692580274282214 chr16 90354753 1183185337 13.094887625889475 29.645247682778447 chr17 81195210 1539873474 18.965077792150545 61.36391889542725 chr18 78077248 723258655 9.2633727945944 26.54119601863189 chr19 59128983 666679719 11.275007368213995 24.12999960836385 chr20 63025520 1800148540 28.562216384727964 50.98988663270955 chr21 48129895 263913705 5.483363406464942 14.148571907518942 chr22 51304566 348490236 6.792577409192001 17.540634865533015 chrMT 16571 535020 32.286524651499604 14.394262299509471 chrX 155270560 1146128294 7.3814913400196405 13.845678691978792 chrY 59373566 30582311 0.5150829411189485 11.792335344216648