Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.

ALE, Flask, Isolate	Predicted Mutations	Mean Coverage	Total Reads	Percent Mapped	Mapped Reads	Average Read Length
A4 F8 I0 R1	24	67.1	3369429	96.5%	3251498	61.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	1,763,636	A→G	31.2%	noncoding (208/1542 nt)	rrsG ←	16S ribosomal RNA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,763,636	0	A	G	31.2%	41.0 / 25.0	32	noncoding (208/1542 nt)	rrsG	16S ribosomal RNA
Reads supporting (aligned to +/- strand): ref base A (15/7); new base G (5/5); total (20/12)
Fisher's exact test for biased strand distribution p-value = 4.38e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAAGGTCCCCCTCTTTGGTCTTGCGACATTATGCGGTATTAGCTACCGTTTCCAGTAGTTATCCCCCTCCAT  >  minE/1763569‑1763705

cTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAAGGt                                                                    >  1:2777303/1‑71 (MQ=255)

cTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAAGGt                                                                    >  1:1636842/1‑71 (MQ=255)

   ggTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAAGGTc                                                                   <  1:2206684/69‑1 (MQ=40)

       aGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTCCCCctc                                                             <  1:158512/71‑1 (MQ=255)

        gCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTccc                                                                 >  1:1970223/1‑66 (MQ=255)

         ccGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTCCCCCTCtt                                                           <  1:43822/71‑1 (MQ=255)

              aCCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAAGGTCCCCCTCTTTGGt                                                       <  1:976828/70‑1 (MQ=40)

              aCCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAAGGTCCCCCTCTTTGGt                                                       >  1:2893485/1‑70 (MQ=40)

                  caccaACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTcc                                                                  >  1:1793462/1‑55 (MQ=255)

                  caccaACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGACCCCctcat                                                           >  1:1278516/1‑60 (MQ=14)

                    ccaACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTCCCCCTCTTTGGTCTTGCGa                                                >  1:2989899/1‑71 (MQ=255)

                    ccaACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTCCCCCTCTTTGGTCTTGCGa                                                <  1:1157747/71‑1 (MQ=255)

                    ccaACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTCCCCCTCTTTGGTCTTGCGa                                                <  1:1791890/71‑1 (MQ=255)

                      aacaaGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTCCCCCTCTTTGGTCTTGCGAcg                                              >  1:579635/1‑70 (MQ=19)

                      aacaaGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAAGGTCCCCCTCTTTGGTCTTGCGACa                                              >  1:1041905/1‑71 (MQ=38)

                      aacaaGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAAGGTCCCCCTCTTTGGTCTTGCGACa                                              >  1:218385/1‑71 (MQ=38)

                       acaaGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTCCCCCTCTTTGGTCTTGCGAcgt                                             <  1:2179825/71‑3 (MQ=9)

                       acaaGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAAGGTCCCCCTCTTTGGTCTTg                                                   >  1:3009666/1‑65 (MQ=35)

                       acaaGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAAGGTCCCCCTCTTTGGTCTTg                                                   >  1:181571/1‑65 (MQ=35)

                         aaGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAAGGTCCCCCTCTTTGGTCTTGCGACATTa                                           <  1:1761268/71‑1 (MQ=35)

                            cTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAAGGTCCCCCTCTTTGGTCTTGCGACATTATGc                                        >  1:915298/1‑71 (MQ=34)

                                tCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAAGGTCCCCCTCTTTGGTCTTGCGACATTATGCGGTa                                    <  1:43607/71‑1 (MQ=34)

                                tCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAAGGTCCCCCTCTTTGGTCTTGCGACATTATGCGGTa                                    <  1:1030898/71‑1 (MQ=34)

                                    aTCTGGGCACATCCGATGGCAAGAGGCCCGAAGGTCCCCCTCTTTGGTCTTGCGACATTATGCGGTATTAg                                >  1:2539050/1‑71 (MQ=34)

                                     tCTGGGCACATCCGATGGCAAGAGGCCCGAAGGTCCCCCTCTTTGGTCTTGCGACATTATGCGGTATTAGc                               >  1:142386/1‑71 (MQ=34)

                                       tGGGCACATCCGATGGCAAGAGGCCCGAAGGTCCCCCTCTTTGGTCTTGCGACATTATGCGGTATTAGCTa                             >  1:2335769/1‑71 (MQ=34)

                                            acaTCCGATGGCAAGAGGCCCGAAGGTCCCCCTCTTTGGTCTTGCGACATTATGCGGTATTAGCTACCGtt                        >  1:1465068/1‑71 (MQ=34)

                                              aTCCGATGGCAAGAGGCCCGAAGGTCCCCCTCTTTGGTCTTGCGACATTATGCGGTATTAGCTACCGTTTc                      <  1:1349632/71‑1 (MQ=34)

                                               tCCGATGGCAAGAGGCCCGAAGGTCCCCCTCTTTTGTCTTGCGACATTATGCGGTATTAGCTACCGTTTc                      >  1:2841885/1‑70 (MQ=25)

                                               tCCGATGGCAAGAGGCCCGAAGGTCCCCCTCTTTGGTCTTGCGACATTATGCGGTATTAGCTACCGTTTc                      >  1:3157502/1‑70 (MQ=35)

                                                        aaGAGCCCCGAAGGTCCCCCTCTTTGGTCTTGCGACATTATGCGGTATTAGCTAc                            >  1:3008714/1‑55 (MQ=255)

                                                                cGAAGGTCCCCCTCTTTGGTCTTGCGACATTATGCGGTATTAGCTACCGtt                        <  1:344219/51‑1 (MQ=35)

                                                                  aaGGTCCCCCTCTTTGGTCTTGCGACATTATGCGGTATTAGCTACCGTTTCCAGTAGTTATCCCCCTCCAt  <  1:3119900/71‑1 (MQ=34)

                                                                   aGGTCCCCCTCTTTGGTCTTGCGACATTATGCGGTATTAGCTACCGTTTCCag                   <  1:1193812/53‑1 (MQ=35)

CTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAAGGTCCCCCTCTTTGGTCTTGCGACATTATGCGGTATTAGCTACCGTTTCCAGTAGTTATCCCCCTCCAT  >  minE/1763569‑1763705

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 21 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A