BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472470.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 = 16,378,418 number of mapped reads = 16,102,511 (98.32%) number of supplementary alignments = 54,243 (0.33%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,071,571 number of mapped paired reads (second in pair) = 8,030,940 number of mapped paired reads (both in pair) = 15,993,068 number of mapped paired reads (singletons) = 109,443 number of mapped bases = 1,575,211,634 bp number of sequenced bases = 1,575,007,974 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,057,703 duplication rate = 46.73% >>>>>>> Insert size mean insert size = 28,510.5241 std insert size = 1,664,501.1441 median insert size = 220 >>>>>>> Mapping quality mean mapping quality = 54.9399 >>>>>>> ACTG content number of A's = 430,260,037 bp (27.32%) number of C's = 359,959,034 bp (22.85%) number of T's = 426,962,815 bp (27.11%) number of G's = 357,578,509 bp (22.7%) number of N's = 247,579 bp (0.02%) GC percentage = 45.56% >>>>>>> Mismatches and indels general error rate = 0.0058 number of mismatches = 8,964,014 number of insertions = 77,660 mapped reads with insertion percentage = 0.48% number of deletions = 76,697 mapped reads with deletion percentage = 0.47% homopolymer indels = 44.62% >>>>>>> Coverage mean coverageData = 0.5088X std coverageData = 17.8708X There is a 5.05% of reference with a coverageData >= 1X There is a 2.38% of reference with a coverageData >= 2X There is a 1.01% of reference with a coverageData >= 3X There is a 0.72% of reference with a coverageData >= 4X There is a 0.5% of reference with a coverageData >= 5X There is a 0.44% of reference with a coverageData >= 6X There is a 0.38% of reference with a coverageData >= 7X There is a 0.36% of reference with a coverageData >= 8X There is a 0.34% of reference with a coverageData >= 9X There is a 0.32% of reference with a coverageData >= 10X There is a 0.31% of reference with a coverageData >= 11X There is a 0.3% of reference with a coverageData >= 12X There is a 0.29% of reference with a coverageData >= 13X There is a 0.28% of reference with a coverageData >= 14X There is a 0.28% of reference with a coverageData >= 15X There is a 0.27% of reference with a coverageData >= 16X There is a 0.26% of reference with a coverageData >= 17X There is a 0.26% of reference with a coverageData >= 18X There is a 0.25% of reference with a coverageData >= 19X There is a 0.24% of reference with a coverageData >= 20X There is a 0.24% of reference with a coverageData >= 21X There is a 0.23% of reference with a coverageData >= 22X There is a 0.23% of reference with a coverageData >= 23X There is a 0.22% of reference with a coverageData >= 24X There is a 0.22% of reference with a coverageData >= 25X There is a 0.22% of reference with a coverageData >= 26X There is a 0.21% of reference with a coverageData >= 27X There is a 0.21% of reference with a coverageData >= 28X There is a 0.21% of reference with a coverageData >= 29X There is a 0.2% of reference with a coverageData >= 30X There is a 0.2% of reference with a coverageData >= 31X There is a 0.2% of reference with a coverageData >= 32X There is a 0.19% of reference with a coverageData >= 33X There is a 0.19% of reference with a coverageData >= 34X There is a 0.19% of reference with a coverageData >= 35X There is a 0.18% of reference with a coverageData >= 36X There is a 0.18% of reference with a coverageData >= 37X There is a 0.18% of reference with a coverageData >= 38X There is a 0.18% of reference with a coverageData >= 39X There is a 0.17% of reference with a coverageData >= 40X There is a 0.17% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.17% of reference with a coverageData >= 43X There is a 0.16% of reference with a coverageData >= 44X There is a 0.16% of reference with a coverageData >= 45X There is a 0.16% of reference with a coverageData >= 46X There is a 0.16% of reference with a coverageData >= 47X There is a 0.16% of reference with a coverageData >= 48X There is a 0.15% of reference with a coverageData >= 49X There is a 0.15% of reference with a coverageData >= 50X There is a 0.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 156877687 0.6293973767070373 20.080852330196286 chr2 243199373 115929451 0.47668482681491126 15.757049521669664 chr3 198022430 198354848 1.001678688621284 22.862986165019812 chr4 191154276 48916717 0.255901767010433 10.849927521209068 chr5 180915260 90816612 0.5019842549489745 17.430693805521773 chr6 171115067 117408957 0.6861403794442017 22.737739775484602 chr7 159138663 69250987 0.4351612970381685 13.437206083483035 chr8 146364022 50478174 0.3448810254749627 10.42988419759955 chr9 141213431 92240070 0.6531961538417688 17.190344421627348 chr10 135534747 41197941 0.3039658973945626 12.534014395649 chr11 135006516 67923515 0.5031128645672184 16.155731083044923 chr12 133851895 81895370 0.6118357158858304 22.92292441217479 chr13 115169878 30260083 0.2627430325141093 10.068892883387774 chr14 107349540 40237365 0.3748256862581805 12.802543420527874 chr15 102531392 35392740 0.3451893055348356 9.55456901534626 chr16 90354753 53151495 0.5882534480504861 17.977830438521824 chr17 81195210 52731532 0.6494414140932698 15.499292055703302 chr18 78077248 23560614 0.30176030282214866 10.353963243259587 chr19 59128983 37318704 0.6311406370713327 17.401713624817685 chr20 63025520 32009811 0.5078865037527656 14.60470414588562 chr21 48129895 6523948 0.13554876859797846 4.631046543529553 chr22 51304566 21685544 0.4226825347280006 16.419816644396363 chrMT 16571 4761 0.2873091545471004 0.8012533078911904 chrX 155270560 109107180 0.7026907096876575 36.14133935982939 chrY 59373566 1937528 0.03263283866089498 1.8677569129883167