BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472723.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 = 10,666,124 number of mapped reads = 10,566,541 (99.07%) number of supplementary alignments = 42,027 (0.39%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,306,017 number of mapped paired reads (second in pair) = 5,260,524 number of mapped paired reads (both in pair) = 10,499,280 number of mapped paired reads (singletons) = 67,261 number of mapped bases = 1,040,999,960 bp number of sequenced bases = 1,040,839,716 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,435,417 duplication rate = 45.91% >>>>>>> Insert size mean insert size = 28,803.2972 std insert size = 1,677,273.9953 median insert size = 239 >>>>>>> Mapping quality mean mapping quality = 54.5451 >>>>>>> ACTG content number of A's = 304,142,085 bp (29.22%) number of C's = 217,426,292 bp (20.89%) number of T's = 302,416,082 bp (29.06%) number of G's = 216,652,188 bp (20.82%) number of N's = 203,069 bp (0.02%) GC percentage = 41.7% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 6,149,418 number of insertions = 73,536 mapped reads with insertion percentage = 0.68% number of deletions = 62,140 mapped reads with deletion percentage = 0.58% homopolymer indels = 42.28% >>>>>>> Coverage mean coverageData = 0.3363X std coverageData = 20.5284X There is a 2.74% of reference with a coverageData >= 1X There is a 1.28% of reference with a coverageData >= 2X There is a 0.62% of reference with a coverageData >= 3X There is a 0.42% of reference with a coverageData >= 4X There is a 0.31% of reference with a coverageData >= 5X There is a 0.25% of reference with a coverageData >= 6X There is a 0.22% of reference with a coverageData >= 7X There is a 0.2% of reference with a coverageData >= 8X There is a 0.18% of reference with a coverageData >= 9X There is a 0.17% of reference with a coverageData >= 10X There is a 0.16% of reference with a coverageData >= 11X There is a 0.15% of reference with a coverageData >= 12X There is a 0.14% of reference with a coverageData >= 13X There is a 0.14% of reference with a coverageData >= 14X There is a 0.13% of reference with a coverageData >= 15X There is a 0.13% of reference with a coverageData >= 16X There is a 0.12% of reference with a coverageData >= 17X There is a 0.12% of reference with a coverageData >= 18X There is a 0.12% of reference with a coverageData >= 19X There is a 0.11% of reference with a coverageData >= 20X There is a 0.11% of reference with a coverageData >= 21X There is a 0.11% of reference with a coverageData >= 22X There is a 0.11% of reference with a coverageData >= 23X There is a 0.1% of reference with a coverageData >= 24X There is a 0.1% of reference with a coverageData >= 25X There is a 0.1% of reference with a coverageData >= 26X There is a 0.1% of reference with a coverageData >= 27X There is a 0.09% of reference with a coverageData >= 28X There is a 0.09% of reference with a coverageData >= 29X There is a 0.09% of reference with a coverageData >= 30X There is a 0.09% of reference with a coverageData >= 31X There is a 0.09% of reference with a coverageData >= 32X There is a 0.09% of reference with a coverageData >= 33X There is a 0.09% of reference with a coverageData >= 34X There is a 0.08% of reference with a coverageData >= 35X There is a 0.08% of reference with a coverageData >= 36X There is a 0.08% of reference with a coverageData >= 37X There is a 0.08% of reference with a coverageData >= 38X There is a 0.08% of reference with a coverageData >= 39X There is a 0.08% of reference with a coverageData >= 40X There is a 0.08% of reference with a coverageData >= 41X There is a 0.08% of reference with a coverageData >= 42X There is a 0.08% of reference with a coverageData >= 43X There is a 0.07% of reference with a coverageData >= 44X There is a 0.07% of reference with a coverageData >= 45X There is a 0.07% of reference with a coverageData >= 46X There is a 0.07% of reference with a coverageData >= 47X There is a 0.07% of reference with a coverageData >= 48X There is a 0.07% of reference with a coverageData >= 49X There is a 0.07% of reference with a coverageData >= 50X There is a 0.07% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 89637728 0.35962890539799297 25.80052235757106 chr2 243199373 115501898 0.47492679185484576 21.81437784062952 chr3 198022430 154767939 0.7815677193740124 28.240933607234382 chr4 191154276 38919271 0.20360136228393866 14.22857181870765 chr5 180915260 70865513 0.3917055587240126 24.03474198233072 chr6 171115067 84497129 0.49380297411215107 23.41299840312834 chr7 159138663 26439045 0.16613841351677058 18.520554577750108 chr8 146364022 60527042 0.4135377066913343 30.62552826150859 chr9 141213431 91888279 0.6507049531287148 24.451673823621483 chr10 135534747 23330073 0.1721335193845162 22.089674792213856 chr11 135006516 33310103 0.24672959488859042 11.7465619230692 chr12 133851895 46071378 0.3441966809659288 16.346428430260648 chr13 115169878 13529443 0.11747379814016995 12.622230571283186 chr14 107349540 20352199 0.1895881342388612 11.421408963049858 chr15 102531392 11048342 0.10775570081014797 7.550285680421094 chr16 90354753 59730679 0.6610684774933755 32.7127122442582 chr17 81195210 11267687 0.13877280445484408 6.294767667528612 chr18 78077248 3965822 0.05079356792903356 1.7849939023813022 chr19 59128983 6056147 0.10242264779017085 6.489382500657273 chr20 63025520 9783322 0.15522794575911472 7.1190051545033874 chr21 48129895 6977714 0.14497671353739708 15.852818317522212 chr22 51304566 4594175 0.08954709801073066 4.002204213744659 chrMT 16571 1931 0.11652887574678655 0.5579370551903856 chrX 155270560 54078435 0.3482851803973657 21.604446711573775 chrY 59373566 3858666 0.0649896285495131 5.206815883352946