BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004048.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 3,083,224 number of mapped reads = 2,658,848 (86.24%) number of supplementary alignments = 31,868 (1.03%) number of secondary alignments = 0 number of mapped bases = 175,578,759 bp number of sequenced bases = 175,499,139 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 221,075 duplication rate = 6.75% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 37.0148 >>>>>>> ACTG content number of A's = 49,004,112 bp (27.92%) number of C's = 32,166,871 bp (18.33%) number of T's = 55,742,081 bp (31.76%) number of G's = 38,443,821 bp (21.91%) number of N's = 142,254 bp (0.08%) GC percentage = 40.23% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,494,493 number of insertions = 11,632 mapped reads with insertion percentage = 0.43% number of deletions = 47,600 mapped reads with deletion percentage = 1.77% homopolymer indels = 46.28% >>>>>>> Coverage mean coverageData = 0.0567X std coverageData = 0.462X There is a 3.81% of reference with a coverageData >= 1X There is a 1.16% of reference with a coverageData >= 2X There is a 0.39% of reference with a coverageData >= 3X There is a 0.14% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 34535587 0.13855767685329057 0.8439343745892186 chr2 243199373 2306616 0.009484465241610635 0.36526925072545946 chr3 198022430 1353316 0.006834155100510584 0.15061132438141983 chr4 191154276 4320371 0.022601487606795676 0.20771047419041738 chr5 180915260 2935623 0.016226508476952138 0.1710280219496894 chr6 171115067 14474679 0.08459032424070523 0.4946732612993831 chr7 159138663 4628902 0.029087224391221637 0.28226132652068836 chr8 146364022 25128059 0.17168193833864445 0.825531978362966 chr9 141213431 3286540 0.02327356524607068 0.239984271588364 chr10 135534747 25250962 0.18630618759335568 0.9244651051085577 chr11 135006516 2328322 0.01724599722283034 0.19325468091272985 chr12 133851895 12304706 0.09192776837414218 0.4124463982477232 chr13 115169878 7125270 0.061867478925348864 0.3396553425805273 chr14 107349540 1397635 0.013019478239031114 0.17587468472556458 chr15 102531392 2745897 0.026781036972559586 0.23038271355044315 chr16 90354753 788323 0.008724754081282255 0.14838327476081334 chr17 81195210 4748074 0.05847726731663112 0.34994263726921043 chr18 78077248 4565504 0.058474192123165 0.5209112262560321 chr19 59128983 641130 0.01084290592314094 0.48200543527748835 chr20 63025520 1520968 0.02413257359875809 0.22289954906949552 chr21 48129895 406073 0.008437022353778249 0.11653583019138347 chr22 51304566 214998 0.004190621162256786 0.08103390019066786 chrMT 16571 152601 9.208919196186109 7.344178861649315 chrX 155270560 17997833 0.1159127203508508 0.5118750192146333 chrY 59373566 420770 0.007086823789563187 0.10957664814333443