BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084895.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,291,871 number of mapped reads = 2,042,877 (89.14%) number of supplementary alignments = 14,560 (0.64%) number of secondary alignments = 0 number of mapped bases = 138,442,222 bp number of sequenced bases = 138,390,898 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 103,029 duplication rate = 4.46% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.3722 >>>>>>> ACTG content number of A's = 39,348,314 bp (28.43%) number of C's = 24,969,609 bp (18.04%) number of T's = 44,672,347 bp (32.28%) number of G's = 29,379,223 bp (21.23%) number of N's = 21,405 bp (0.02%) GC percentage = 39.27% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 1,116,231 number of insertions = 10,359 mapped reads with insertion percentage = 0.5% number of deletions = 29,330 mapped reads with deletion percentage = 1.42% homopolymer indels = 48.81% >>>>>>> Coverage mean coverageData = 0.0447X std coverageData = 0.3037X There is a 3.81% of reference with a coverageData >= 1X There is a 0.52% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% 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 11687564 0.046890811959100394 0.412830695833034 chr2 243199373 11716423 0.0481762056187538 0.3538827398994639 chr3 198022430 11662688 0.058895792764486324 0.2768003717250982 chr4 191154276 8370060 0.04378693574189259 0.23811882311771176 chr5 180915260 5806722 0.03209636378932324 0.20679532396450148 chr6 171115067 8514395 0.049758300944942505 0.26526636955837785 chr7 159138663 7765971 0.04880002667862052 0.3417754787240256 chr8 146364022 8149325 0.05567847131175447 0.4633827140320275 chr9 141213431 9272038 0.06565974592034379 0.37801086770300224 chr10 135534747 4802058 0.03543045681119691 0.23049309416601657 chr11 135006516 6135192 0.0454436732520377 0.2715255973693838 chr12 133851895 6230744 0.046549538951241594 0.2474878317710787 chr13 115169878 3351037 0.029096470867148092 0.19291149275894495 chr14 107349540 2830873 0.026370611369177736 0.19540218377211507 chr15 102531392 3562075 0.034741311226906976 0.211124935405172 chr16 90354753 2420411 0.026787865824833806 0.20004518552073924 chr17 81195210 2869719 0.035343451910525264 0.21620544555347793 chr18 78077248 5455635 0.06987483728934708 0.5340904770556925 chr19 59128983 2650425 0.04482446451006945 0.3273185034319666 chr20 63025520 2928215 0.046460782870177034 0.24594487038654772 chr21 48129895 1310467 0.027227713669435598 0.19507289005525738 chr22 51304566 1299059 0.025320533848780632 0.1767544468211406 chrMT 16571 54522 3.290205781183996 2.403838998344656 chrX 155270560 9294641 0.05986093564678327 0.29476856837999477 chrY 59373566 301963 0.005085815462052591 0.1144068259812325