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 F3 I0 R2	8	43.3	2136430	96.9%	2070200	62.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	1,763,636	A→G	23.3%	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	23.3%	55.8 / 15.4	30	noncoding (208/1542 nt)	rrsG	16S ribosomal RNA
Reads supporting (aligned to +/- strand): ref base A (9/14); new base G (5/2); total (14/16)
Fisher's exact test for biased strand distribution p-value = 2.04e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.33e-01

GCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAAGGTCCCCCTCTTTGGTCTTGCGACATTATGCGGTATTAGCTACCGTTTCCAGTAGTTATCCCCCTCCAT  >  minE/1763567‑1763705

gCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAAg                                                                      >  1:315252/1‑71 (MQ=255)

   ttGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTc                                                                   >  1:178832/1‑71 (MQ=255)

          gCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTCCCCctct                                                            <  1:482710/71‑1 (MQ=255)

          gCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAAGGTCCCCctc                                                             <  1:1342247/70‑1 (MQ=40)

                aCCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTCCCCCTCTTTGGTc                                                      >  1:200395/1‑71 (MQ=255)

                aCCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAAg                                                                      >  1:8200/1‑55 (MQ=255)

                 ccccACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAAGGTCCCCCTCTTTGGTc                                                      <  1:1506417/70‑1 (MQ=40)

                    caccaACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTCCCCCTCTTTGGTCTTg                                                   >  1:1754783/1‑70 (MQ=255)

                    caccaACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTCCCCCTCTTTGGTCTTGc                                                  >  1:1563970/1‑71 (MQ=255)

                       caacaaGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAAGGt                                                                    <  1:763135/50‑1 (MQ=255)

                        aacaaGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAAGGTCCCCCTCTTTGGTCTTGCGACa                                              <  1:1439655/71‑1 (MQ=38)

                         acaaGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTCCCCCTCTTTGGTCTTGCGAcgt                                             <  1:412254/71‑3 (MQ=9)

                         acaaGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAGGGTCCCCCTCTTTGGTCTTGCGAcgt                                             >  1:1881482/1‑69 (MQ=9)

                          caaGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAAGGTCCCCCTCTTTGGTCTTGCGACAt                                             >  1:1681103/1‑70 (MQ=37)

                             gCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAAGGTCCCCCTCTTTGGTCTTGCGACATTATg                                         <  1:1988121/71‑1 (MQ=34)

                                 aTCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAAGGTCCCCCTCTTTGGTCTTGCGACATTATGCgg                                      <  1:1701684/70‑1 (MQ=35)

                                      aTCTGGGCACATCCGATGGCAAGAGGGCCGAAGGTCCCCCTCTTTGGTCTTGCGACATTATGCGGTATTAg                                <  1:2040953/71‑1 (MQ=255)

                                       tCTGGGCACATCCGATGGCAAGAGGCCCGAAGGTCCCCCTCTTTGGTCTTGCGACATTATGCGGTATTAGc                               >  1:768523/1‑71 (MQ=34)

                                         tGGGCACATCCGATGGCAAGAGGCCCGAAGGTCCCCCTCTTTGGTCTTGCGACATTATGCGGTATTAGCTa                             >  1:675085/1‑71 (MQ=34)

                                           ggCACATCCGATGGCAAGAGGCCCGAAGGTCCCCCTCTTTGGTCTTGCGACATTATGCGGTATTAGCt                              <  1:313693/68‑1 (MQ=35)

                                           ggCACATCCGATGGCAAGAGGCCCGAAGGTCCCCCTCTTTGGTCTTGCGACATTATGCGGTATTAGCTAcc                           <  1:290930/71‑1 (MQ=34)

                                                aTCCGATGGCAAGAGGCCCGAAGGTCCCCCTCTTTGGTCTTGCGACAt                                             <  1:194234/48‑1 (MQ=35)

                                                aTCCGATGGCAAGAGGCCCGAAGGTCCCCCTCTTTGGTCTTGCGACATTATGCGGTATTAGCt                              <  1:504842/63‑1 (MQ=35)

                                                 tCCGATGGCAAGAGGCCCGAAGGTCCCCCTCTTTGGTCTTGCGACa                                              <  1:1787604/46‑1 (MQ=32)

                                                  ccGATGGCAAGAGGCCCGAAGGTCCCCCTCTTTGGTCTTGCGACATTATGCGGTATTa                                 >  1:671207/1‑58 (MQ=35)

                                                     aTGGCAAGAGGCCCGAAGGTCCCCCTCTTTGGTCTTGCGACATTATGCGGTATTAGCTACCGTTTCCag                   >  1:414178/1‑69 (MQ=35)

                                                      tGGCAAGAGGCCCGAAGGTCCCCCTCTTTGGTCTTGCGACATTATGCGGTATTAGCTACCTTTTCCa                    <  1:563245/67‑1 (MQ=25)

                                                            gagGCCCGAAGGTCCCCCTCTTTGGTCTTGCGACATTATGCGGTATTAGCTACCGTTTCCag                   <  1:1629624/62‑1 (MQ=35)

                                                             agGCCCGAAGGTCCCCCTCTTTGGTCTTGCGACATTATGCGGTATTAGCTACCGTTTCCAGTAGTTATcc          >  1:545373/1‑70 (MQ=35)

                                                                  cGAAGGTCCCCCTCTTTGGTCTTGCGACATTATGCGGTATTAGCTa                             >  1:1631804/1‑46 (MQ=38)

                                                                     aGGTCCCCCTCTTTGGTCTTGCGACATTATGCGGTATTAGCTACCGTTTCCAGTAGTTATCACCCTCCAt  >  1:1680850/1‑70 (MQ=25)

GCCTTGGTGAGCCGTTACCCCACCAACAAGCTAATCCCATCTGGGCACATCCGATGGCAAGAGGCCCGAAGGTCCCCCTCTTTGGTCTTGCGACATTATGCGGTATTAGCTACCGTTTCCAGTAGTTATCCCCCTCCAT  >  minE/1763567‑1763705

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A