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
A2 F1 I0 R1	4577	57.4	3436498	77.7%	2670158	63.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	390,468	G→A	37.6%	H333H (CAC→CAT)	ybdN ←	conserved hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	390,468	0	G	A	37.6%	35.1 / 35.3	61	H333H (CAC→CAT)	ybdN	conserved hypothetical protein
Reads supporting (aligned to +/- strand): ref base G (29/9); new base A (19/4); total (48/13)
Fisher's exact test for biased strand distribution p-value = 7.49e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GATATCTTTCGCGCCAATGTCCCCTTGCTGGGTTTGTGGAACCTCGATGCCTTTTTTCTGATACCAGTGCAAATAAATGGCGATTTTATTGCGGTAATGCTCAGCTG‑TTTTTTCCGGCATGCTATTGAGCA  >  minE/390402‑390532

gATATCTTTCGCGCCAATGTCCCCTTGCTGGGTTTGTGGAACCTCGATGCCTTTTTTCTGATACCAg                                                                   >  1:3335068/1‑67 (MQ=255)

gATATCTTTCGCGCCAATGTCCCCTTGCTGGGTTTGTGGAACCTCGATGCCTTTTTTCTGATACCAGt                                                                  >  1:2105034/1‑68 (MQ=255)

                aTGTCCCCGTGCTGGGTCTGTGGCACCTCGACACCTTTTTTCTGATACCAATGCAAGTAAATGGcaa                                                   >  1:493522/1‑65 (MQ=255)

                aTGTCCCCGTGCTGGGTCTGTGGCACCTCGACACCTTTTTTCTGATACCAATGCAAGTAAATGGcaa                                                   >  1:2663050/1‑65 (MQ=255)

                aTGTCCCCGTGCTGGGTCTGTGGCACCTCGACACCTTTTTTCTGATACCAATGCAAGTAAATGGcaa                                                   >  1:1546246/1‑65 (MQ=255)

                aTGTCCCCGTGCTGGGTCTGTGGCACCTCGACACCTTTTTTCTGATACCAATGCAAGTAAATGGCAAtt                                                 >  1:76408/1‑69 (MQ=255)

                aTGTCCCCGTGCTGGGTCTGTGGCACCTCGACACCTTTTTTCTGATACCAATGCAAGTAAATGGCAAtt                                                 >  1:234022/1‑69 (MQ=255)

                aTGTCCCCGTGCTGGGTCTGTGGCACCTCGACACCTTTTTTCTGATACCAATGCAAGTAAATGGCAAtt                                                 >  1:2542416/1‑69 (MQ=255)

                aTGTCCCCGTGCTGGGTCTGTGGCACCTCGACACCTTTTTTCTGATACCAATGCAAGTAAATGGCAAtt                                                 >  1:1860803/1‑69 (MQ=255)

                aTGTCCCCGTGCTGGGTCTGTGGCACCTCGACACCTTTTTTCTGATACCAATGCAAGTAAATGGCAAtt                                                 >  1:3263806/1‑69 (MQ=255)

                aTGTCCCCGTGCTGGGTCTGTGGCACCTCGACACCTTTTTTCTGATACCAATGCAAGTAAATGGCAAtt                                                 >  1:1255411/1‑69 (MQ=255)

                aTGTCCCCGTGCTGGGTCTGTGGCACCTCGACACCTTTTTTCTGATACCAATGCAAGTAAATGGCAAtt                                                 >  1:1213377/1‑69 (MQ=255)

                aTGTCCCCGTGCTGGGTCTGTGGCACCTCGACACCTTTTTTCTGATACCAATGCAAGTAAATGGCAAtt                                                 >  1:601329/1‑69 (MQ=255)

                aTGTCCCCGTGCTGGGTCTGTGGCACCTCGACACCTTTTTTCTGATACCAATGCAAGTAAATGGCAAt                                                  >  1:1547293/1‑68 (MQ=255)

                aTGTCCCCGTGCTGGGTCTGTGGCACCTCGACACCTTTTTTCTGATACCAATGCAAGTAAATGGCAAt                                                  >  1:3087890/1‑68 (MQ=255)

                aTGTCCCCGTGCTGGGTCTGTGGCACCTCGACACCTTTTTTCTGATACCAATGCAAGTAAATGGCAAt                                                  >  1:2776372/1‑68 (MQ=255)

                aTGTCCCCGTGCTGGGTCTGTGGCACCTCGACACCTTTTTTCTGATACCAATGCAAGTAAATGGCAAt                                                  >  1:1416713/1‑68 (MQ=255)

                aTGTCCCCGTGCTGGGTCTGTGGCACCTCGACACCTTTTTTCTGATACCAATGCAAGTAAATGGCAAt                                                  >  1:2581629/1‑68 (MQ=255)

                aTGTCCCCGTGCTGGGTCTGTGGCACCTCGACACCTTTTTTCTGATACCAATGCAAGTAAATGGCAAt                                                  >  1:2463874/1‑68 (MQ=255)

                aTGTCCCCGTGCTGGGTCTGTGGCACCTCGACACCTTTTTTCTGATACCAATGCAAGTAAATGGCAAt                                                  >  1:2355805/1‑68 (MQ=255)

                aTGTCCCAGTGCTGGGTCTGTGGCACCTCGACACCTTTTTTCTGATACCAATGCAAGTAAATGGCAAtt                                                 >  1:2627298/1‑69 (MQ=255)

                 tGTCCCCTTGCTGGGTTTGTGGAACCTCGATGCCTTTTTTCTGATACCAGTGCAAATAAATGGCGAttt                                                <  1:3037099/69‑1 (MQ=255)

                 tGTCCCCTTGCTGGGTTTGTGGAACCTCGATGCCTTTTTTCTGATACCAGTGCAAATAAATGGCGAttt                                                <  1:2878199/69‑1 (MQ=255)

                 tGTCCCCTTGCTGGGTTTGTGGAACCTCGATGCCTTTTTTCTGATACCAGTGCAAATAAATGGCGAttt                                                <  1:271046/69‑1 (MQ=255)

                 tGTCCCCTTGCTGGGTTTGTGGAACCTCGATGCCTTTTTTCTGATACCAGTGCAAATAAATGGCGAttt                                                <  1:1163178/69‑1 (MQ=255)

                 tGTCCCCTTGCTGGGTTTGTGGAACCTCGATGCCTTTTTTCTGATACCAGTGCAAATAAATGGCGAttt                                                <  1:1757446/69‑1 (MQ=255)

                   tCCCCTTGCTGGGTTTGTGGAACCTCGATGCCTTTTTTCTGATACCAGTGCAAATAAATGGCGATTTTa                                              >  1:2839368/1‑69 (MQ=255)

                   tCCCCTTGCTGGGTTTGTGGAACCTCGATGCCTTTTTTCTGATACCAGTGCAAATAAATGGCGATTTTa                                              >  1:175856/1‑69 (MQ=255)

                          gCTGGGTTTGTGGAACCTCGATGCCTTTTTTCTGATACCAGTGCAAATAAATGGCGATTTTATTGCGGt                                       >  1:2410886/1‑69 (MQ=255)

                          gCTGGGTTTGTGGAACCTCGATGCCTTTTTTCTGATACCAGTGCAAATAAATGGCGATTTTATTGCGGt                                       >  1:1809174/1‑69 (MQ=255)

                            tGGGTTTGTGGAACCTCGATGCCTTTTTTCTGATACCAGTGCAAATAAATGGCGATTTTATTGCGGt                                       <  1:1804006/67‑1 (MQ=255)

                                  tgtgGAACCTCGATGCCTTTTTTCTGATACCAGTGCAAATAAATGGCGAtttt                                               >  1:940696/1‑53 (MQ=255)

                                  tgtgGAACCTCGATGCCTTTTTTCTGATACCAGTGCAAATAAATGGCGAtttt                                               >  1:1348518/1‑53 (MQ=255)

                                  tgtgGAACCTCGATGCCTTTTTTCTGATACCAGTGCAAATAAATGGCGAtttt                                               >  1:1777180/1‑53 (MQ=255)

                                  tgtgGAACCTCGATGCCTTTTTTCTGATACCAGTGCAAATAAATGGCGAtttt                                               >  1:2647228/1‑53 (MQ=255)

                                  tgtgGAACCTCGATGCCTTTTTTCTGATACCAGTGCAAATAAATGGCGAtttt                                               >  1:625339/1‑53 (MQ=255)

                                  tgtgGAACCTCGATGCCTTTTTTCTGATACCAGTGCAAATAAATGGCGAtttt                                               >  1:638408/1‑53 (MQ=255)

                                  tgtgGAACCTCGATGCCTTTTTTCTGATACCAGTCCAAATAAATGGCGAtttt                                               >  1:1196759/1‑53 (MQ=255)

                                        aCCTCGACACCTTTTTTCTGATACCAATGCAAGTAAATGGCAATTTTGTTGCGGTAATGCTCAGCGG‑t                         <  1:2727004/68‑1 (MQ=255)

                                        aCCTCGACACCTTTTTTCTGATACCAATGCAAGTAAATGGCAATTTTGTTGCGGTAATGCTCAGCGG‑t                         <  1:1541861/68‑1 (MQ=255)

                                        aCCTCGACACCTTTTTTCTGATACCAATGCAAGTAAATGGCAATTTTGTTGCGGTAATGCTCAGCGG‑t                         <  1:3221653/68‑1 (MQ=255)

                                        aCCTCGACACCTTTTTTCTGATACCAATGCAAGTAAATGGCAATTTTGTTGCGGTAATGCTCAGCGG‑t                         <  1:3148511/68‑1 (MQ=255)

                                                gCCTTTTTTCTGATACCAGTGCAAATAAATGGCGAttt                                                >  1:528662/1‑38 (MQ=255)

                                                gCCTTTTTTCTGATACCAGTGCAAATAAATGGCGAttt                                                >  1:665918/1‑38 (MQ=255)

                                                gCCTTTTTTCTGATACCAGTGCAAATAAATGGCGAttt                                                >  1:173406/1‑38 (MQ=255)

                                                gCCTTTTTTCTGATACCAGTGCAAATAAATGGCGAttt                                                >  1:467081/1‑38 (MQ=255)

                                                gCCTTTTTTCTGATACCAGTGCAAATAAATGGCGAttt                                                >  1:2284691/1‑38 (MQ=255)

                                                       ttCTGATACCAGTGCAAATAAATGGCGATTTTATTGCGGTAATGCTCAGCTG‑TTTTTTCCGGCATGc           <  1:2921800/67‑1 (MQ=255)

                                                       ttCTGATACCAGTGCAAATAAATGGCGATTTTATTGCGGTAATGCTCAGCTG‑TTTTTTCCGGCATGc           <  1:2577741/67‑1 (MQ=255)

                                                        tCTGATACCAGTGCAAATAAATGGCGATTTTATTGCGGTAATGCTCAGCTG‑TTTTTTCCGGCATGc           <  1:1007592/66‑1 (MQ=255)

                                                            aTACCAGTGCAAATAAATGGCGATTTTATTGCGGTAATGCTCAGCTGTTTTTTTCCGGCATGCTATTg      >  1:2617503/1‑68 (MQ=255)

                                                            aTACCAGTGCAAATAAATGGCGATTTTATTGCGGTAATGCTCAGCTG‑TTTTTTCCGGCATGCTATTg      >  1:1496973/1‑67 (MQ=255)

                                                            aTACCAGTGCAAATAAATGGCGATTTTATTGCGGTAATGCTCAGCTG‑TTTTTTCCGGCATGCTATTg      >  1:186598/1‑67 (MQ=255)

                                                              acaaGTGCAAATAAATGGCGATTTTATTGCGGTAATGCTCAGCTG‑TTTTTTCCGGCATGCTATTGagc   >  1:2784897/4‑68 (MQ=255)

                                                              aCCAGTGCAAATAAATGGCGATTTTATTGCGGTAATGCTCAGCTG‑TTTTTTCCGGCATGCTATTGagc   >  1:1680580/1‑68 (MQ=255)

                                                              aCCAGTGCAAATAAATGGCGATTTTATTGCGGTAATGCTCAGCTG‑TTTTTTCCGGCATGCTATTGagc   >  1:357313/1‑68 (MQ=255)

                                                              aCCAGTGCAAATAAATGGCGATTTTATTGCGGTAATGCTCAGCTG‑TTTTTTCCGGCATGCTATTGagc   >  1:1922719/1‑68 (MQ=255)

                                                              aCCAGTGCAAATAAATGGCGATTTTATTGCGGTAATGCTCAGCTG‑TTTTTTCCGGCATGCTATTGagc   >  1:1995700/1‑68 (MQ=255)

                                                              aCCAGTGCAAATAAATGGCGATTTTATTGCGGTAATGCTCAGCTG‑TTTTTTCCGGCATGCTATTGagc   >  1:846548/1‑68 (MQ=255)

                                                              aCCAGTGCAAATAAATGGCGATTTTATTGCGGTAATGCTCAGCTG‑TTTTTTCCGGCATGCTATTGagc   >  1:2181756/1‑68 (MQ=255)

                                                              aCCAGTGCAAATAAATGGCGATTTTATTGCGGTAATGCTCAGCTG‑TTTTTTCCGGCAGGCTATTGagc   >  1:3076934/1‑68 (MQ=255)

                                                              aCCAGTGCAAATAAATGGCGATTTTATTGCGGT‑ATGCTCAGCTG‑TTTTTTCCGGCATGCTATTGagca  >  1:401556/1‑68 (MQ=255)

GATATCTTTCGCGCCAATGTCCCCTTGCTGGGTTTGTGGAACCTCGATGCCTTTTTTCTGATACCAGTGCAAATAAATGGCGATTTTATTGCGGTAATGCTCAGCTG‑TTTTTTCCGGCATGCTATTGAGCA  >  minE/390402‑390532

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