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	1,829,862	T→G	35.8%	S146R (AGT→AGG) ‡	pphB →	serine/threonine‑specific protein phosphatase 2

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,829,862	0	T	G	35.8%	32.4 / 42.3	53	S146R (AGT→AGG) ‡	pphB	serine/threonine‑specific protein phosphatase 2
Reads supporting (aligned to +/- strand): ref base T (18/16); new base G (14/5); total (32/21)
Fisher's exact test for biased strand distribution p-value = 1.58e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.70e-01

ATATTATTGAAATCACTAACGACAACATAAAATATGCCATCGCACATGCAGATTATCCGGGGAGTGAATATCTCTTTGGTAAAGAAATAGCGGAGAGCGAATTACTCTGGCCTGTTGATCGTGTGCAGAA  >  minE/1829798‑1829927

atatTATTGAAATCACTAACGACACCATAAAATATGTCATCGCGCATGCAGATTATCCGGGGAAGGAat                                                               >  1:1131611/1‑69 (MQ=255)

atatTATTGAAATCACTAACGACACCATAAAATATGTCATCGCACATGCAGATTATCCGGGGAAGGAat                                                               >  1:2569050/1‑69 (MQ=255)

atatTATTGAAATCACTAACGACACCATAAAATATGTCATCGCACATGCAGATTATCCGGGGAAGGAat                                                               >  1:2642739/1‑69 (MQ=255)

atatTATTGAAATCACTAACGACACCATAAAATATGTCATCGCACATGCAGATTATCCGGGGAAGGAat                                                               >  1:492035/1‑69 (MQ=255)

atatTATTGAAATCACTAACGACACCATAAAATATGTCATCGCACATGCAGATTATCCGGGGAAGGAat                                                               >  1:455349/1‑69 (MQ=255)

atatTATTGAAATCACTAACGACACCATAAAATATGTCATCGCACATGCAGATTATCCGGGGAAGGAat                                                               >  1:38391/1‑69 (MQ=255)

atatTATTGAAATCACTAACGACACCATAAAATATGTCATCGCACATGCAGATTATCCGGGGAAGGAat                                                               >  1:2889281/1‑69 (MQ=255)

atatTATTGAAATCACTAACGACACCATAAAATATGTCATCGCACATGCAGATTATCCGGGGAAGGAat                                                               >  1:3007294/1‑69 (MQ=255)

atatTATTGAAATCACTAACGACACCATAAAATATGTCATCGCACATGCAGATTATCCGGGGAAGGAat                                                               >  1:3078514/1‑69 (MQ=255)

           aTCACTAACGACAACATAAAATATGCCATCGCACATGCAGATTATCCGGGGAGTGAATATCTCTTTgg                                                     >  1:1689629/1‑68 (MQ=255)

           aTCACTAACGACAACATAAAATATGCCATCGCACATGCAGATTATCCGGGGAGTGAATATCTCTTTgg                                                     >  1:2535826/1‑68 (MQ=255)

           aTCACTAACGACAACATAAAATATGCCATCGCACATGCAGATTATCCGGGGAGTGAATATCTCTTTgg                                                     >  1:2730288/1‑68 (MQ=255)

           aTCACTAACGACAACATAAAATATGCCATCGCACATGCAGATTATCCGGGGAGTGAATATCTCTTTgg                                                     >  1:2863092/1‑68 (MQ=255)

           aTCACTAACGACAACATAAAATATGCCATCGCACATGCAGATTATCCGGGGAGTGAATATCTCTTTgg                                                     >  1:3181492/1‑68 (MQ=255)

           aTCACTAACGACAACATAAAATATGCCATCGCACATGCAGATTATCCGGGGAGTGAATATCTCTTTgg                                                     >  1:3354747/1‑68 (MQ=255)

           aTCACTAACGACAACATAAAATATGCCATCGCACATGCAGATTATCCGGGGAGTGAATATCTCTTTgg                                                     >  1:1210369/1‑68 (MQ=255)

           aTCACTAACGACAACATAAAATATGCCATCGCACATGCAGATTATCCGGGGAGTGAATATCTCTTTgg                                                     >  1:1000253/1‑68 (MQ=255)

           aTCACTAACGACAACATAAAATATGCCATCGCACATGCAGATTATCCGGGGAGTGAATATCTCTTTg                                                      >  1:2169174/1‑67 (MQ=255)

             cACTAACGACAACATAAAATATGCCATCGCACATGCAGATTATCCGGGGAGTGAATATCTCTTTgg                                                     >  1:3162262/1‑66 (MQ=255)

             cACTAACGACAACATAAAATATGCCATCGCACATGCAGATTATCCGGGGAGTGAATATCTCTTTgg                                                     >  1:3059921/1‑66 (MQ=255)

             cACTAACGACAACATAAAATATGCCATCGCACATGCAGATTATCCGGGGAGTGAATATCTCTTTgg                                                     >  1:2485230/1‑66 (MQ=255)

                tAACGACAACATAAAATATGCCATCGCACATGCAGATTATCCGGGGAGTGAATATCTCTTTGGTAAAGa                                               <  1:1245858/69‑1 (MQ=255)

                tAACGACAACATAAAATATGCCATCGCACATGCAGATTATCCGGGGAGTGAATATCTCTTTGGTAAAGa                                               <  1:61972/69‑1 (MQ=255)

                tAACGACAACATAAAATATGCCATCGCACATGCAGATTATCCGGGGAGTGAATATCTCTTTGGTAAAGa                                               <  1:1096971/69‑1 (MQ=255)

                                    ccATCGCACATGCAGATTATCCGGGGAGTGAATATCTCTTTGGTAAAGAAATAGCGGAGAGCGAATTa                            <  1:1024594/68‑1 (MQ=255)

                                    ccATCGCACATGCAGATTATCCGGGGAGTGAATATCTCTTTGGTAAAGAAATAGCGGAGAGCGAATTa                            <  1:1949555/68‑1 (MQ=255)

                                    ccATCGCACATGCAGATTATCCGGGGAGTGAATATCTCTTTGGTAAAGAAATAGCGGAGAGCGAATTa                            <  1:1945561/68‑1 (MQ=255)

                                    ccATCGCACATGCAGATTATCCGGGGAGTGAATATCTCTTTGGTAAAGAAATAGCGGAGAGCGAATTa                            <  1:1873970/68‑1 (MQ=255)

                                    ccATCGCACATGCAGATTATCCGGGGAGTGAATATCTCTTTGGTAAAGAAATAGCGGAGAGCGAATTa                            <  1:1844049/68‑1 (MQ=255)

                                            caTGCAGATTATCCGGGGAGTGAATATCTCTTTGGTAAAGAAATAGCGGAGAGCGAATTACTCTGGcc                    >  1:1147105/1‑68 (MQ=255)

                                            caTGCAGATTATCCGGGGAGTGAATATCTCTTTGGTAAAGAAATAGCGGAGAGCGAATTACTCTGGCCt                   >  1:980497/1‑69 (MQ=255)

                                            caTGCAGATTATCCGGGGAGTGAATATCTCTTTGGTAAAGAAATAGCGGAGAGCGAATTACTCTGGCCt                   >  1:1325913/1‑69 (MQ=255)

                                            caTGCAGATTATCCGGGGAGTGAATATCTCTTTGGTAAAGAAATAGCGGAGAGCGAATTACTCTGGCCt                   >  1:3262612/1‑69 (MQ=255)

                                             aTGCAGATTATCCGGGGAGTGAATATCTCTTTGGTAAAGAAATAGCGGAGAGCGAATTACTCTGGCCTg                  <  1:944500/69‑1 (MQ=255)

                                                    ttATCCGGGGAAGGAGTATCAGTTTGGCAAAGAAATAGCGGAGAGCGAATTACTCTGGCCTGTTGATCg           >  1:67493/1‑69 (MQ=255)

                                                    ttATCCGGGGAAGGAGTATCAGTTTGGCAAAGAAATAGCGGAGAGCGAATTACTCTGGCCTGTTGATCg           >  1:1768110/1‑69 (MQ=255)

                                                    ttATCCGGGGAAGGAGTATCAGTTTGGCAAAGAAATAGCGGAGAGCGAATTACTCTGGCCTGTTGATCg           >  1:307941/1‑69 (MQ=255)

                                                    ttATCCGGGGAAGGAGTATCAGTTTGGCAAAGAAATAGCGGAGAGCGAATTACTCTGGCCTGTTGATCg           >  1:1756966/1‑69 (MQ=255)

                                                    ttATCCGGGGAAGGAGTATCAGTTTGGCAAAGAAATAGCGGAGAGCGAATTACTCTGGCCTGTTGATCg           >  1:1632986/1‑69 (MQ=255)

                                                     tATCCGGGGAGTGAATATCTCTTTGGTAAAGAAATAGCGGAGAGCGAATTACTCTgg                      <  1:3238235/57‑1 (MQ=255)

                                                     tATCCGGGGAGTGAATATCTCTTTGGTAAAGAAATAGCGGAGAGCGAATTACTCTgg                      <  1:1268467/57‑1 (MQ=255)

                                                     tATCCGGGGAGTGAATATCTCTTTGGTAAAGAAATAGCGGAGAGCGAATTACTCTgg                      <  1:3016252/57‑1 (MQ=255)

                                                     tATCCGGGGAGTGAATATCTCTTTGGTAAAGAAATAGCGGAGAGCGAATTACTCTgg                      <  1:3012315/57‑1 (MQ=255)

                                                     tATCCGGGGAGTGAATATCTCTTTGGTAAAGAAATAGCGGAGAGCGAATTACTCTgg                      <  1:2890198/57‑1 (MQ=255)

                                                     tATCCGGGGAGTGAATATCTATTTGGTAAAGAAATAGCGGAGAGCGAATTACTCTgg                      <  1:1107266/57‑1 (MQ=255)

                                                        ccGGGGAAGGAGTATCAGTTTGGCAAAGAAATAGCGGAGAGCGAATTACTCTGGCCTGTTGATCgtgt        <  1:1395852/68‑1 (MQ=255)

                                                        ccGGGGAAGGAGTATCAGTTTGGCAAAGAAATAGCGGAGAGCGAATTACTCTGGCCTGTTGATCgtgt        <  1:3393192/68‑1 (MQ=255)

                                                        ccGGGGAAGGAGTATCAGTTTGGCAAAGAAATAGCGGAGAGCGAATTACTCTGGCCTGTTGATCgtgt        <  1:2413416/68‑1 (MQ=255)

                                                        ccGGGGAAGGAGTATCAGTTTGGCAAAGAAATAGCGGAGAGCGAATTACTCTGGCCTGTTGATCgtgt        <  1:1937453/68‑1 (MQ=255)

                                                        ccGGGGAAGGAGTATCAGTTTGGCAAAGAAATAGCGGAGAGCGAATTACTCTGGCCTGTTGATCgtgt        <  1:989294/68‑1 (MQ=255)

                                                         cGGGGAGTGAATATCTCTTTGGTAAAGAAATAGCGGAGAGCGAATTACTCTGGCCTGTTGATCgtg         >  1:3302957/1‑66 (MQ=255)

                                                         cGGGGAGTGAATATCTCTTTGGTAAAGAAATAGCGGAGAGCGAATTACTCTGGCCTGTTGATCgtg         >  1:1780682/1‑66 (MQ=255)

                                                             gAGTGAATATCTCTTTGGTAAAGAAATAGCGGAGAGCGAATTACTCTGGCCTGTTGATCGTGTGCAGaa  <  1:685486/69‑1 (MQ=255)

ATATTATTGAAATCACTAACGACAACATAAAATATGCCATCGCACATGCAGATTATCCGGGGAGTGAATATCTCTTTGGTAAAGAAATAGCGGAGAGCGAATTACTCTGGCCTGTTGATCGTGTGCAGAA  >  minE/1829798‑1829927

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A