BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926996.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 35,811,108 number of mapped reads = 31,658,816 (88.41%) number of supplementary alignments = 877,879 (2.45%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,841,848 number of mapped paired reads (second in pair) = 15,816,968 number of mapped paired reads (both in pair) = 31,124,678 number of mapped paired reads (singletons) = 534,138 number of mapped bases = 2,938,914,090 bp number of sequenced bases = 2,936,641,721 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,856,583 duplication rate = 7.35% >>>>>>> Insert size mean insert size = 284,000.295 std insert size = 5,210,731.2695 median insert size = 200 >>>>>>> Mapping quality mean mapping quality = 52.8894 >>>>>>> ACTG content number of A's = 836,387,601 bp (28.48%) number of C's = 581,790,476 bp (19.81%) number of T's = 849,051,798 bp (28.91%) number of G's = 669,092,836 bp (22.78%) number of N's = 319,010 bp (0.01%) GC percentage = 42.6% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 27,187,612 number of insertions = 495,008 mapped reads with insertion percentage = 1.54% number of deletions = 1,570,461 mapped reads with deletion percentage = 4.83% homopolymer indels = 52.64% >>>>>>> Coverage mean coverageData = 0.9494X std coverageData = 3.0076X There is a 35.6% of reference with a coverageData >= 1X There is a 20.53% of reference with a coverageData >= 2X There is a 12.41% of reference with a coverageData >= 3X There is a 7.93% of reference with a coverageData >= 4X There is a 5.21% of reference with a coverageData >= 5X There is a 3.52% of reference with a coverageData >= 6X There is a 2.42% of reference with a coverageData >= 7X There is a 1.69% of reference with a coverageData >= 8X There is a 1.2% of reference with a coverageData >= 9X There is a 0.86% of reference with a coverageData >= 10X There is a 0.62% of reference with a coverageData >= 11X There is a 0.45% of reference with a coverageData >= 12X There is a 0.34% of reference with a coverageData >= 13X There is a 0.25% of reference with a coverageData >= 14X There is a 0.19% of reference with a coverageData >= 15X There is a 0.14% of reference with a coverageData >= 16X There is a 0.11% of reference with a coverageData >= 17X There is a 0.09% of reference with a coverageData >= 18X There is a 0.07% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 242621790 0.9734049569328856 3.7234353536265408 chr2 243199373 254473535 1.0463576935290866 4.862873263737045 chr3 198022430 199455457 1.0072366903082646 1.9837963704837682 chr4 191154276 176690755 0.9243358751755049 2.424983954479642 chr5 180915260 177585128 0.9815928628685054 1.9312601387122486 chr6 171115067 170689472 0.9975128139943399 2.3106235612594666 chr7 159138663 151323349 0.9508899103921716 2.6501369422484142 chr8 146364022 149376435 1.020581649498536 2.1476367569533616 chr9 141213431 126181609 0.8935524624424712 3.697466395599166 chr10 135534747 143146470 1.0561606759040174 5.301430207414421 chr11 135006516 140521143 1.0408471173346923 2.8948083638392856 chr12 133851895 132281491 0.9882675997975224 2.015542180194643 chr13 115169878 88372470 0.7673227716712524 1.7150557473009003 chr14 107349540 88618554 0.8255140543685608 1.834385871191501 chr15 102531392 88035078 0.858615847134895 1.9262212391739097 chr16 90354753 91196037 1.009310899228511 3.475513570989144 chr17 81195210 75682415 0.9321044307909296 2.371964258339454 chr18 78077248 78076806 0.999994338939815 3.5610840825012935 chr19 59128983 48979532 0.8283506584241437 2.6211586795765185 chr20 63025520 69361595 1.1005318956511585 2.2362529936891367 chr21 48129895 38336879 0.7965294543027779 3.0036594873367597 chr22 51304566 37221407 0.7254989156325774 1.8201997136163843 chrMT 16571 294767 17.788123830788727 15.131622761544788 chrX 155270560 165557824 1.0662537959546228 2.2760318246323332 chrY 59373566 4834092 0.0814182526951472 2.1423585798392306