BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524462.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 = 2,945,054 number of mapped reads = 2,716,634 (92.24%) number of supplementary alignments = 6,237 (0.21%) number of secondary alignments = 0 number of mapped bases = 158,409,641 bp number of sequenced bases = 158,359,064 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 162,441 duplication rate = 4.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3471 >>>>>>> ACTG content number of A's = 40,680,065 bp (25.69%) number of C's = 29,342,599 bp (18.53%) number of T's = 50,792,927 bp (32.07%) number of G's = 37,540,247 bp (23.71%) number of N's = 3,226 bp (0%) GC percentage = 42.23% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 741,266 number of insertions = 10,542 mapped reads with insertion percentage = 0.39% number of deletions = 29,417 mapped reads with deletion percentage = 1.08% homopolymer indels = 43.05% >>>>>>> Coverage mean coverageData = 0.0512X std coverageData = 0.4289X There is a 4.26% of reference with a coverageData >= 1X There is a 0.6% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 15594148 0.06256412897763652 0.8260014629013919 chr2 243199373 12632166 0.05194160595142653 0.4825607638508421 chr3 198022430 8722339 0.044047227377221866 0.24697536623482305 chr4 191154276 8987721 0.04701815302316334 0.3037179348651957 chr5 180915260 8614154 0.04761430296150806 0.25677869490363825 chr6 171115067 6889051 0.040259756903814906 0.31987553071473973 chr7 159138663 7881472 0.049525815106288784 0.5800254258922525 chr8 146364022 14564336 0.0995076235333298 0.45326985261857294 chr9 141213431 6685996 0.047346742817968926 0.3737078640009151 chr10 135534747 8281040 0.06109901839415394 0.43574872300825224 chr11 135006516 5383304 0.03987440132148881 0.40092243663764443 chr12 133851895 7302513 0.054556665036382186 0.27351613019746385 chr13 115169878 3570839 0.031004973366386652 0.20949374082910951 chr14 107349540 3758730 0.0350139367155183 0.22724390530204253 chr15 102531392 4147661 0.04045259621560585 0.25549328659791315 chr16 90354753 4925808 0.054516313048855326 0.3003555747696152 chr17 81195210 5465081 0.06730792370633687 0.32898776082376524 chr18 78077248 3786137 0.04849219326992673 0.6818516709789803 chr19 59128983 3188406 0.05392289598486752 0.5610501141492419 chr20 63025520 4499615 0.07139354026749799 0.31888239150656417 chr21 48129895 2191573 0.045534547706783904 0.281443109198067 chr22 51304566 1278670 0.024923122826923435 0.18205428573386015 chrMT 16571 70855 4.2758433407760545 3.17515873511076 chrX 155270560 9482875 0.06107323242731912 0.34089934159214275 chrY 59373566 505151 0.008508011797708092 0.20975435994448796