BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124946.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 4,124,364 number of mapped reads = 4,020,115 (97.47%) number of supplementary alignments = 20,118 (0.49%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,013,048 number of mapped paired reads (second in pair) = 2,007,067 number of mapped paired reads (both in pair) = 4,003,408 number of mapped paired reads (singletons) = 16,707 number of mapped bases = 354,329,937 bp number of sequenced bases = 354,138,423 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 290,902 duplication rate = 5% >>>>>>> Insert size mean insert size = 51,959.5226 std insert size = 2,119,936.083 median insert size = 214 >>>>>>> Mapping quality mean mapping quality = 52.7856 >>>>>>> ACTG content number of A's = 100,915,559 bp (28.5%) number of C's = 65,584,476 bp (18.52%) number of T's = 106,311,265 bp (30.02%) number of G's = 81,322,075 bp (22.96%) number of N's = 5,048 bp (0%) GC percentage = 41.48% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 2,589,100 number of insertions = 48,360 mapped reads with insertion percentage = 1.17% number of deletions = 114,414 mapped reads with deletion percentage = 2.79% homopolymer indels = 48.48% >>>>>>> Coverage mean coverageData = 0.1145X std coverageData = 1.1326X There is a 8.18% of reference with a coverageData >= 1X There is a 2.02% of reference with a coverageData >= 2X There is a 0.53% of reference with a coverageData >= 3X There is a 0.18% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 30386035 0.12190956587426115 1.2195018823797228 chr2 243199373 30350902 0.12479843852229011 1.1798844718355805 chr3 198022430 24592948 0.12419273917606202 0.44398601217759676 chr4 191154276 21024092 0.10998494221494684 0.6841727448519793 chr5 180915260 19629939 0.10850350047862187 0.42354822760109223 chr6 171115067 15677008 0.09161675984967473 0.8664112370495507 chr7 159138663 35442159 0.2227124341241952 2.9753320901162144 chr8 146364022 28972174 0.19794600889008093 0.6817604830722859 chr9 141213431 13526819 0.09578988984411829 1.55955694506276 chr10 135534747 16537117 0.12201385523669439 1.6194990759932217 chr11 135006516 15961104 0.11822469368811798 0.8506323011591774 chr12 133851895 18151384 0.1356079717810495 0.472769958796923 chr13 115169878 7332892 0.06367022460508294 0.3117657063008703 chr14 107349540 9780011 0.09110435871453199 0.46390180576310386 chr15 102531392 8545409 0.08334431858683826 0.36669248404578997 chr16 90354753 8826451 0.0976866264024871 1.247497283669548 chr17 81195210 7917318 0.09750966836590484 1.1217148585359953 chr18 78077248 8324032 0.10661277405679052 1.55479437273932 chr19 59128983 4126534 0.0697886855249988 0.6929273859263365 chr20 63025520 6990305 0.11091229394061326 0.45706932216156465 chr21 48129895 4322748 0.08981419967776784 0.4850186028227753 chr22 51304566 3167685 0.061742750148203185 0.3294292152177822 chrMT 16571 372331 22.468831090459236 15.981561767398208 chrX 155270560 10913256 0.07028541663017124 0.4829251285291735 chrY 59373566 3459284 0.05826303240738479 1.1458924819018321