BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618639.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 66,398,612 number of mapped reads = 59,034,321 (88.91%) number of supplementary alignments = 320,796 (0.48%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 31,971,569 number of mapped paired reads (second in pair) = 27,062,752 number of mapped paired reads (both in pair) = 53,442,358 number of mapped paired reads (singletons) = 5,591,963 number of mapped bases = 5,423,964,540 bp number of sequenced bases = 5,420,125,598 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,045,487 duplication rate = 18.23% >>>>>>> Insert size mean insert size = 156,500.2018 std insert size = 3,940,226.5876 median insert size = 227 >>>>>>> Mapping quality mean mapping quality = 53.2452 >>>>>>> ACTG content number of A's = 1,462,211,173 bp (26.98%) number of C's = 1,181,463,043 bp (21.8%) number of T's = 1,504,407,840 bp (27.76%) number of G's = 1,271,720,934 bp (23.46%) number of N's = 322,608 bp (0.01%) GC percentage = 45.26% >>>>>>> Mismatches and indels general error rate = 0.0151 number of mismatches = 80,444,148 number of insertions = 1,012,607 mapped reads with insertion percentage = 1.68% number of deletions = 2,754,088 mapped reads with deletion percentage = 4.55% homopolymer indels = 52.07% >>>>>>> Coverage mean coverageData = 1.7521X std coverageData = 7.3983X There is a 32.18% of reference with a coverageData >= 1X There is a 21.89% of reference with a coverageData >= 2X There is a 16.35% of reference with a coverageData >= 3X There is a 12.86% of reference with a coverageData >= 4X There is a 10.42% of reference with a coverageData >= 5X There is a 8.64% of reference with a coverageData >= 6X There is a 7.28% of reference with a coverageData >= 7X There is a 6.22% of reference with a coverageData >= 8X There is a 5.37% of reference with a coverageData >= 9X There is a 4.67% of reference with a coverageData >= 10X There is a 4.09% of reference with a coverageData >= 11X There is a 3.61% of reference with a coverageData >= 12X There is a 3.2% of reference with a coverageData >= 13X There is a 2.85% of reference with a coverageData >= 14X There is a 2.56% of reference with a coverageData >= 15X There is a 2.3% of reference with a coverageData >= 16X There is a 2.07% of reference with a coverageData >= 17X There is a 1.87% of reference with a coverageData >= 18X There is a 1.7% of reference with a coverageData >= 19X There is a 1.55% of reference with a coverageData >= 20X There is a 1.41% of reference with a coverageData >= 21X There is a 1.29% of reference with a coverageData >= 22X There is a 1.18% of reference with a coverageData >= 23X There is a 1.09% of reference with a coverageData >= 24X There is a 1% of reference with a coverageData >= 25X There is a 0.92% of reference with a coverageData >= 26X There is a 0.85% of reference with a coverageData >= 27X There is a 0.79% of reference with a coverageData >= 28X There is a 0.73% of reference with a coverageData >= 29X There is a 0.67% of reference with a coverageData >= 30X There is a 0.63% of reference with a coverageData >= 31X There is a 0.58% of reference with a coverageData >= 32X There is a 0.54% of reference with a coverageData >= 33X There is a 0.51% of reference with a coverageData >= 34X There is a 0.47% of reference with a coverageData >= 35X There is a 0.44% of reference with a coverageData >= 36X There is a 0.41% of reference with a coverageData >= 37X There is a 0.39% of reference with a coverageData >= 38X There is a 0.36% of reference with a coverageData >= 39X There is a 0.34% of reference with a coverageData >= 40X There is a 0.32% of reference with a coverageData >= 41X There is a 0.3% of reference with a coverageData >= 42X There is a 0.28% of reference with a coverageData >= 43X There is a 0.27% of reference with a coverageData >= 44X There is a 0.25% of reference with a coverageData >= 45X There is a 0.24% of reference with a coverageData >= 46X There is a 0.22% of reference with a coverageData >= 47X There is a 0.21% of reference with a coverageData >= 48X There is a 0.2% of reference with a coverageData >= 49X There is a 0.19% of reference with a coverageData >= 50X There is a 0.18% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 484351076 1.9432291645122923 7.932086995575565 chr2 243199373 445590123 1.8322009530838717 10.268600342502593 chr3 198022430 342896844 1.7316060811898935 5.828974422888566 chr4 191154276 276874297 1.4484337091156674 5.521320658154147 chr5 180915260 306041658 1.6916298713552411 5.79547847604202 chr6 171115067 294945976 1.7236704001056786 5.810354672723544 chr7 159138663 279146436 1.7541082144192703 6.068362708023348 chr8 146364022 255674757 1.7468415632907381 6.1965356473084485 chr9 141213431 230504609 1.6323136359458612 7.294966480795949 chr10 135534747 259528198 1.9148462202094936 6.849593487238929 chr11 135006516 282711805 2.09406044520103 7.150289463722005 chr12 133851895 246859283 1.8442718573390389 6.7678555320965526 chr13 115169878 145004707 1.2590506260673473 4.986453714014864 chr14 107349540 161084615 1.5005617630033627 5.638953090152429 chr15 102531392 174354493 1.7004986433813363 6.51014328939262 chr16 90354753 203638660 2.25376810005778 17.435114203673272 chr17 81195210 184985221 2.2782775116906526 7.367557832591935 chr18 78077248 134428683 1.721739513667285 6.889020080592679 chr19 59128983 116770847 1.974849575883962 7.114040390996819 chr20 63025520 148200155 2.3514308965638047 7.5023909925233445 chr21 48129895 68445548 1.4221005053096418 7.645129795079578 chr22 51304566 91610022 1.785611479492878 6.857734210770371 chrMT 16571 10983 0.662784382354716 1.6977523706296647 chrX 155270560 280809319 1.8085161733170796 5.640145732254297 chrY 59373566 9496225 0.15994028386302417 5.948800795336367