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	1,903,827	G→T	57.3%	R699R (CGA→AGA)	ptr ←	protease III

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,903,827	0	G	T	57.3%	10.1 / 64.0	61	R699R (CGA→AGA)	ptr	protease III
Reads supporting (aligned to +/- strand): ref base G (13/13); new base T (20/15); total (33/28)
Fisher's exact test for biased strand distribution p-value = 6.13e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.08e-01

GCGTGCCAGCGTTGTTGCCTGGGCCTCGGTCATGTTGCCGATAACCATAAACTCTGGTCGAGCCCCTGATTTTAAGGCGTCGCGATAGGCCAGCACCTCTTTCAACGTAATGGAGGGCAAAATTT  >  minE/1903768‑1903892

gcgTGCCAGCGTTGTTGCCTGGGCCTCGGTCATGTTGCCGATAACCATAAACTCTGGTCGAGCCCCTGa                                                          >  1:2179599/1‑69 (MQ=255)

gcgTGCCAGCGTTGTTGCCTGGGCCTCGGTCATGTTGCCGATAACCATAAACTCTGGTCGAGCCCCTGa                                                          >  1:2734180/1‑69 (MQ=255)

gcgTGCCAGCGTTGTTGCCTGGGCCTCGGTCATGTTGCCGATAACCATAAACTCTGGTCGAGCCCCTGa                                                          >  1:3431889/1‑69 (MQ=255)

gcgTGCCAGCGTTGTTGCCTGGGCCTCGGTCATGTTGCCGATAACCATAAACTCTGGTCGAGCCCCTGa                                                          >  1:1264466/1‑69 (MQ=255)

     ccAGCGTTGTTGCCTGGGCCTCGGTCATGTTGCCGATAACCATAAACTCTGGTCGAGCCCCTGAtttt                                                      >  1:1266886/1‑68 (MQ=255)

           ttgttgCCTGGGCCTCGGTCATGTTGCCGATAACCATAAACTCTGGTCGAGCCCCTGATTTTAAGGCGt                                               <  1:1360548/69‑1 (MQ=255)

           ttgttgCCTGGGCCTCGGTCATGTTGCCGATAACCATAAACTCTGGTCGAGCCCCTGATTTTAAGGCGt                                               <  1:1389543/69‑1 (MQ=255)

               tgCCTGGGCCTCGGTCATGTTGCCGATAACCATAAACTCTGGTCGAGCCCCTGATTTTAAGGCGTcgc                                            <  1:2848140/68‑1 (MQ=255)

                gCCTGGGCTTCAGTCATGTTGCCGATAACCATAAACTCTGGTCTAGCCCCTGATTTTAAGGCGTcgcg                                           <  1:3413407/68‑1 (MQ=255)

                gCCTGGGCTTCAGTCATGTTGCCGATAACCATAAACTCTGGTCTAGCCCCTGATTTTAAGGCGTcgcg                                           <  1:1358304/68‑1 (MQ=255)

                gCCTGGGCTTCAGTCATGTTGCCGATAACCATAAACTCTGGTCTAGCCCCTGATTTTAAGGCGTcgcg                                           <  1:3141866/68‑1 (MQ=255)

                gCCTGGGCTTCAGTCATGTTGCCGATAACCATAAACTCTGGTCTAGCCCCTGATTTTAAGGCGTcgcg                                           <  1:2851565/68‑1 (MQ=255)

                gCCTGGGCTTCAGTCATGTTGCCGATAACCATAAACTCTGGTCTAGCCCCTGATTTTAAGGCGTcgcg                                           <  1:560702/68‑1 (MQ=255)

                gCCTGGGCTTCAGTCATGTTGCCGATAACCATAAACTCTGGTCTAGCCCCTGATTTTAAGGCGTcgcg                                           <  1:2440/68‑1 (MQ=255)

                gCCTGGGCTTCAGTCATGTTGCCGATAACCATAAACTCTGGTCTAGCCCCTGATTTTAAGGCGTcgcg                                           <  1:2368091/68‑1 (MQ=255)

                gCCTGGGCTTCAGTCATGTTGCCGATAACCATAAACTCTGGTCTAGCCCCTGATTTTAAGGCGTcgcg                                           <  1:2211227/68‑1 (MQ=255)

                gCCTGGGCTTCAGTCATGTTGCCGATAACCATAAACTCTGGTCTAGCCCCTGATTTTAAGGCGTcgcg                                           <  1:1035350/68‑1 (MQ=255)

                gCCTGGGCTTCAGTCATGTTGCCGATAACCATAAACTCTGGTCTAACCCCTGATTTTAAGGCGTcgcg                                           <  1:3392264/68‑1 (MQ=255)

                      gCCTCGGTCATGTTGCCGATAACCATAAACTCTGGTCGAGCCCCTGATTTTAAGGCGt                                               >  1:3414972/1‑58 (MQ=255)

                      gCCTCGGTCATGTTGCCGATAACCATAAACTCTGGTCGAGCCCCTGATTTTAAGGCGTCGCGATAGGcc                                    >  1:1050422/1‑69 (MQ=255)

                        cTCGGTCATGTTGCCGATAACCATAAACTCTGGTCGAGCCCCTGATTTTAAGGCGTCGCGATAGGCCAg                                  <  1:2360280/69‑1 (MQ=255)

                         tCGGTCATGTTGCCGATAACCATAAACTCTGGTCGAGCCCCTGATTTTAAGGCGTCGCGATAGGCCAGc                                 <  1:3156329/69‑1 (MQ=255)

                         tCGGTCATGTTGCCGATAACCATAAACTCTGGTCGAGCCCCTGATTTTAAGGCGTCGCGATAGGCCAGc                                 <  1:3248867/69‑1 (MQ=255)

                         tCGGTCATGTTGCCGATAACCATAAACTCTGGTCGAGCCCCTGATTTTAAGGCGTCGCGATAGGCCAGc                                 <  1:794326/69‑1 (MQ=255)

                         tCGGTCATGTTGCCGATAACCATAAACTCTGGTCGAGCCCCTGATTTTAAGGCGTCGCGATAGGCCAGc                                 <  1:3410671/69‑1 (MQ=255)

                              cATGTTGCCGATAACCATAAACTCTGGTCGAGCCCCTGATTTTAAGGCGTcgc                                            <  1:1101322/53‑1 (MQ=255)

                               aTGTTGCCGATAACCATAAACTCTGGTCGAGCCCCTGATTTTAAGGCGTCGCGATAGGCCAGCACctct                           >  1:311219/1‑69 (MQ=255)

                                  ttGCCGATAACCATAAACTCTGGTCGAGCCCCTGATTTTAAGGCGTCGCGATAGGcc                                    >  1:2048676/1‑57 (MQ=255)

                                  ttGCCGATAACCATAAACTCTGGTCGAGCCCCTGATTTTAAGGCGTCGCGATAGGCCAGCACCTCttt                         >  1:1353319/1‑68 (MQ=255)

                                  ttGCCGATAACCATAAACTCTGGTCGAGCCCCTGATTTTAAGGCGTCGCGATAGGCCAGCACCTCTTTc                        >  1:273980/1‑69 (MQ=255)

                                  ttGCCGATAACCATAAACTCTGGTCGAGCCCCTGATTTTAAGGCGTCGCGATAGGCCAGCACCTCTTTc                        >  1:1570526/1‑69 (MQ=255)

                                  ttGCCGATAACCATAAACTCTGGTCGAGCCCCTGATTTTAAGGCGTCGCGATAGGCCAGCACCTCTTTc                        <  1:1612531/69‑1 (MQ=255)

                                  ttGCCGATAACCATAAACTCTGGTCGAGCCCCTGATTTTAAGGCGTCGCGATAGGCCAGCACCTCTTTc                        >  1:37793/1‑69 (MQ=255)

                                        aTAACCATAAACTCTGTTCTAGCCCCTGATTTTAAg                                                   >  1:2813768/1‑36 (MQ=38)

                                        aTAACCATAAACTCTGGTCTAGCCCCTGATTTTAAGGCGTCGCGATAGGCCAGCACCTCTTTCAACGt                   >  1:3048466/1‑68 (MQ=255)

                                        aTAACCATAAACTCTGGTCTAGCCCCTGATTTTAAGGCGTCGCGATAGGCCAGCACCTCTTTCAACGTa                  >  1:1149872/1‑69 (MQ=255)

                                        aTAACCATAAACTCTGGTCTAGCCCCTGATTTTAAGGCGTCGCGATAGGCCAGCACCTCTTTCAACGTa                  >  1:2199422/1‑69 (MQ=255)

                                        aTAACCATAAACTCTGGTCTAGCCCCTGATTTTAAGGCGTCGCGATAGGCCAGCACCTCTTTCAACGTa                  >  1:1333842/1‑69 (MQ=255)

                                        aTAACCATAAACTCTGGTCTAGCCCCTGATTTTAAGGCGTCGCGATAGGCCAGCACCTCTTTCAACGTa                  >  1:385591/1‑69 (MQ=255)

                                        aTAACCATAAACTCTGGTCTAGCCCCTGATTTTAAGGCGTCGCGATAGGCCAGCACCTCTTTCAACGTa                  >  1:436078/1‑69 (MQ=255)

                                        aTAACCATAAACTCTGGTCTAGCCCCTGATTTTAAGGCGTCGCGATAGGCCAGCACCTCTTTCAACGTa                  >  1:720865/1‑69 (MQ=255)

                                        aTAACCATAAACTCTGGTCTAGCCCCTGATTTTAAGGCGTCGCGATAGGCCAGCACCTCTTTCAACGTa                  >  1:826616/1‑69 (MQ=255)

                                        aTAACCATAAACTCTGGTCTAGCCCCTGATTTTAAGGCGTCGCGATAGGCCAGCACCTCTTTCAACGTa                  >  1:830493/1‑69 (MQ=255)

                                        aTAACCATAAACTCTGGTCTAGCCCCTGATTTTAAGGCGTCGCGATAGGCCAGCACCTCTTTCAACGTa                  >  1:3135606/1‑69 (MQ=255)

                                        aTAACCATAAACTCTGGTCTAGCCCCTGATTTTAAGGCGTCGCGATAGGCCAGCACCTCTTTCAACGTa                  >  1:3125721/1‑69 (MQ=255)

                                        aTAACCATAAACTCTGGTCTAGCCCCTGATTTTAAGGCGTCGCGATAGGCCAGCACCTCTTTCAACGTa                  >  1:2915645/1‑69 (MQ=255)

                                        aTAACCATAAACTCTGGTCTAGCCCCTGATTTTAAGGCGTCGCGATAGGCCAGCACCTCTTTCAACGTa                  >  1:2872127/1‑69 (MQ=255)

                                        aTAACCATAAACTCTGGTCTAGCCCCTGATTTTAAGGCGTCGCGATAGGCCAGCACCTCTTTCAACGTa                  >  1:2819369/1‑69 (MQ=255)

                                        aTAACCATAAACTCTGGTCTAGCCCCTGATTTTAAGGCGTCGCGATAGGCCAGCACCTCTTTCAACGTa                  >  1:2084886/1‑69 (MQ=255)

                                        aTAACCATAAACTCTGGTCTAGCCCCTGATTTTAAGGCGTCGCGATAGGCCAGCACCTCTTTCAACGTa                  >  1:2566851/1‑69 (MQ=255)

                                        aTAACCATAAACTCTGGTCTAGCCCCTGATTTTAAGGCGTCGCGATAGGCCAGCACCTCTTTCAACGTa                  >  1:1791229/1‑69 (MQ=255)

                                        aTAACCATAAACTCTGGTCTAGCCCCTGATTTTAAGGCGTCGCGATAGGCCAGCACCTCTTTCAACGTa                  >  1:1932236/1‑69 (MQ=255)

                                        aTAACCATAAACTCTGGTCTAGCCCCTGATTTTAAGGCGTCGCGATAGGCCAGCACCTCTTTCAACGTa                  >  1:2237047/1‑69 (MQ=255)

                                             cATAAACTCTGGTCTAGCCCCTGATTTTAAGGCGTCGCGATATGCCAGCACCTCTTTCAACGTAATGGa             <  1:173613/69‑1 (MQ=255)

                                             cATAAACTCTGGTCTAGCCCCTGATTTTAAGGCGTCGCGATAGGCCAGCACCTCTTTCAACGTAATGGa             <  1:1277251/69‑1 (MQ=255)

                                             cATAAACTCTGGTCTAGCCCCTGATTTTAAGGCGTCGCGATAGGCCAGCACCTCTTTCAACGTAATGGa             <  1:3433056/69‑1 (MQ=255)

                                             cATAAACTCTGGTCTAGCCCCTGATTTTAAGGCGTCGCGATAGGCCAGCACCTCTTTCAACGTAATGGa             <  1:415034/69‑1 (MQ=255)

                                             cATAAACTCTGGTCTAGCCCCTGATTTTAAGGCGTCGCGATAGGCCAGCACCTCTTTCAACGTAATGGa             <  1:254810/69‑1 (MQ=255)

                                                          cGAGCCCCTGATTTTAAGGCGTCGCGATAGGCCAGCACGTCTTTCAACGTAATGGAGGGCAAAAttt  <  1:2639262/67‑1 (MQ=255)

                                                          cGAGCCCCTGATTTTAAGGCGTCGCGATAGGCCAGCACCTCTTTCAACGTAATGGAGGGCAAAAttt  <  1:155739/67‑1 (MQ=255)

                                                          cGAGCCCCTGATTTTAAGGCGTCGCGATAGGCCAGCACCTCTTTCAACGTAATGGAGGGCAAAAttt  <  1:968976/67‑1 (MQ=255)

GCGTGCCAGCGTTGTTGCCTGGGCCTCGGTCATGTTGCCGATAACCATAAACTCTGGTCGAGCCCCTGATTTTAAGGCGTCGCGATAGGCCAGCACCTCTTTCAACGTAATGGAGGGCAAAATTT  >  minE/1903768‑1903892

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