BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716908.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,098,603 number of mapped reads = 890,049 (81.02%) number of supplementary alignments = 2,927 (0.27%) number of secondary alignments = 0 number of mapped bases = 49,040,356 bp number of sequenced bases = 49,026,278 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 21,678 duplication rate = 1.71% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 38.0835 >>>>>>> ACTG content number of A's = 11,121,763 bp (22.69%) number of C's = 9,723,383 bp (19.83%) number of T's = 14,534,151 bp (29.65%) number of G's = 13,645,624 bp (27.83%) number of N's = 1,357 bp (0%) GC percentage = 47.67% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 261,486 number of insertions = 4,035 mapped reads with insertion percentage = 0.45% number of deletions = 8,230 mapped reads with deletion percentage = 0.92% homopolymer indels = 34.59% >>>>>>> Coverage mean coverageData = 0.0158X std coverageData = 0.1597X There is a 1.44% of reference with a coverageData >= 1X There is a 0.1% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 4668824 0.018731443802501097 0.19032381890418412 chr2 243199373 4171396 0.017152165930954106 0.20556717236318736 chr3 198022430 3183687 0.016077405978706553 0.14598590070361978 chr4 191154276 2737864 0.014322797571109526 0.15353884681008828 chr5 180915260 3929537 0.021720318120207218 0.1604748100220832 chr6 171115067 2021630 0.011814447643000367 0.12115231168002707 chr7 159138663 2489479 0.015643458057706568 0.1692860999276243 chr8 146364022 2894930 0.019778972731427126 0.16295549695845737 chr9 141213431 2128592 0.015073580359363976 0.1427496837656627 chr10 135534747 2407212 0.0177608477035044 0.21389240482696598 chr11 135006516 1956509 0.014491959780667179 0.15588489383982018 chr12 133851895 2364623 0.01766596580496675 0.14423646945092042 chr13 115169878 857493 0.007445462432459988 0.09303182259842224 chr14 107349540 2208775 0.020575542289235707 0.15948082582918963 chr15 102531392 998732 0.009740743595873545 0.10914912751950993 chr16 90354753 1354141 0.014986937101139549 0.14443528404725473 chr17 81195210 1952204 0.02404333950241646 0.17663672239372522 chr18 78077248 1274015 0.01631736559157413 0.17820203966544496 chr19 59128983 1331676 0.022521544130058857 0.197035816771017 chr20 63025520 1205420 0.01912590328489158 0.15700034506383923 chr21 48129895 629927 0.013088060965019766 0.13532955521547776 chr22 51304566 520834 0.010151805981557275 0.1116249055792417 chrMT 16571 2251 0.13583971999275843 0.39318374252311505 chrX 155270560 1577078 0.010156967296311678 0.12273576520010106 chrY 59373566 173527 0.002922630586143335 0.09946523946810433