BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234025.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 = 2,881,146 number of mapped reads = 512,874 (17.8%) number of supplementary alignments = 4,927 (0.17%) number of secondary alignments = 0 number of mapped bases = 30,995,247 bp number of sequenced bases = 30,979,723 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 102,432 duplication rate = 13.55% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.5271 >>>>>>> ACTG content number of A's = 8,154,193 bp (26.32%) number of C's = 5,348,389 bp (17.26%) number of T's = 10,349,629 bp (33.41%) number of G's = 7,118,593 bp (22.98%) number of N's = 8,919 bp (0.03%) GC percentage = 40.24% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 273,870 number of insertions = 4,978 mapped reads with insertion percentage = 0.95% number of deletions = 8,834 mapped reads with deletion percentage = 1.69% homopolymer indels = 39.34% >>>>>>> Coverage mean coverageData = 0.01X std coverageData = 0.2394X There is a 0.47% of reference with a coverageData >= 1X There is a 0.2% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 2625037 0.010531716990185553 0.23768930957425924 chr2 243199373 3061227 0.012587314524038678 0.2996999365936349 chr3 198022430 2113876 0.010674932127638268 0.22887504620613594 chr4 191154276 2106862 0.011021788495068768 0.22017128423592988 chr5 180915260 1760552 0.009731362628006062 0.2104330561346716 chr6 171115067 1608899 0.009402439120103901 0.2125639064738853 chr7 159138663 1724621 0.010837221876119444 0.23868620456925912 chr8 146364022 1743627 0.011912948115077078 0.2572512114581129 chr9 141213431 1339226 0.009483701306003959 0.19451699730696334 chr10 135534747 1319894 0.009738417853836404 0.2062417421540192 chr11 135006516 1306449 0.00967693292670407 0.20025658057462145 chr12 133851895 1258243 0.009400262880103415 0.20972597456769515 chr13 115169878 967070 0.008396900446486538 0.245059756418832 chr14 107349540 1017084 0.009474507296444865 0.2119304438505206 chr15 102531392 850135 0.008291460628955472 0.19124331900261882 chr16 90354753 876328 0.00969874822191147 0.2030744040578325 chr17 81195210 707394 0.008712262706137468 0.1928088423288869 chr18 78077248 860324 0.01101888222289802 0.5921221648160756 chr19 59128983 558139 0.00943934719797227 0.19473475797460515 chr20 63025520 590183 0.009364190886485348 0.19564933342523128 chr21 48129895 370671 0.007701471195812914 0.1689639189628422 chr22 51304566 317711 0.006192645699410068 0.14496701252916724 chrMT 16571 11335 0.6840263110252851 1.5765604348480164 chrX 155270560 1745456 0.011241384071777676 0.22198088071802963 chrY 59373566 154904 0.0026089724844891413 0.09546557546460685