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
A6 F28 I2 R2	64	60.0	3197630	92.7%	2964203	60.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	minE	1,019,797	T→C	Y249C (TAT→TGT)	uidC ←	predicted outer membrane porin protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,019,797	0	T	C	98.2%	194.0 / ‑4.1	54	Y249C (TAT→TGT)	uidC	predicted outer membrane porin protein
Reads supporting (aligned to +/- strand): ref base T (0/0); major base C (26/27); minor base A (0/1); total (26/28)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.94e-01

GGCTGGTATTACGACTTAAACCTTCGAGCTGCGCGTAAAAGCCGAGCAACTCCCCTTTCAACGTATAATTCGGGTCGAGCGGTATGCTTTTCTCGAGAATACTTTGTATCTGATTGGAAACATCTTTCTG  >  minE/1019732‑1019861

ggctggTATTACGACTTAAACCTTCGAGCTGCGCGTAAAAGCCGAGCAACTCCCCTTTCAACGTACAATTc                                                             >  1:2029175/1‑71 (MQ=255)

  ctggTATTACGACTTAAACCTTCGAGCTGCGCGTAAAAGCCGAGCAACTCCCCTTTCAACGTACAATTCgg                                                           <  1:2869812/71‑1 (MQ=255)

  ctggTATTACGACTTAAACCTTCGAGCTGCGCGTAAAAGCCGAGCAACTCCCCTTTCAACGTACAATTCgg                                                           <  1:31052/71‑1 (MQ=255)

     gTATTACGACTTAAACCTTCGAGCTGCGCGTAAAAGCCGAGCAACTCCCCTTTCAACGTACAATTCGGGTc                                                        >  1:2408132/1‑71 (MQ=255)

      tATTACGACTTAAACCTTCGAGCTGCGCGTAAAAGCCGAGCAACTCCCCTTTCAACGTACAATTCg                                                            <  1:2669264/66‑1 (MQ=255)

      tATTACGACTTAAACCTTCGAGCTGCGCGTAAAAGCCGAGCAACTCCCCTTTCAACGTACAATTCGGGTCg                                                       <  1:2926871/71‑1 (MQ=255)

        ttACGACTTAAACCTTCGAGCTGCGCGTAAAAGCCGAGCAACTCCCCTTTCAACGTACAATTCGGGTCGa                                                      <  1:387571/70‑1 (MQ=255)

        ttACGACTTAAACCTTCGAGCTGCGCGTAAAAGCCGAGCAACTCCCCTTTCAACGTACAATTCGGGTCGAg                                                     <  1:954909/71‑1 (MQ=255)

         tACGACTTAAACCTTCGAGCTGCGCGTAAAAGCCGAGCAACTCCCCTTTCAACGTACAATTCGGGTCGAGc                                                    >  1:3008612/1‑71 (MQ=255)

         tACGACTTAAACCTTCGAGCTGCGCGTAAAAGCCGAGCAAATCCCCTTTCAACGTACAATTCGGGTCGAg                                                     <  1:241252/70‑1 (MQ=255)

             aCTTAAACCTTCGAGCTGCGCGTAAAAGCCGAGCAACTCCCCTTTCAACGTACAATTCGGGTCGAGCGGTa                                                <  1:1401720/71‑1 (MQ=255)

             aCTTAAACCTTCGAGCTGCGCGTAAAAGCCGAGCAACTCCCCTTTCAACGTACAATTCGGGTCGAGCGGTa                                                <  1:1973675/71‑1 (MQ=255)

                 aaaCCTTCGAGCTGCGCGTAAAAGCCGAGCAACTCCCCTTTCAACGTACAATTCGGGTCGAGCGGTATGc                                             <  1:1772613/70‑1 (MQ=255)

                  aaCCTTCGAGCTGCGCGTAAAAGCCGAGCAACTCCCCTTTCAACGTACAATTc                                                             >  1:1439132/1‑53 (MQ=255)

                  aaCCTTCGAGCTGCGCGTAAAAGCCGAGCAACTCCCCTTTCAACGTACAATTc                                                             >  1:64808/1‑53 (MQ=255)

                  aaCCTTCGAGCTGCGCGTAAAAGCCGAGCAACTCCCCTTTCAACGTACAATTCGGGTCGAGCGGTATGCtt                                           <  1:797568/71‑1 (MQ=255)

                       tCGAGCTGCGCGTAAAAGCCGAGCAACTCCCCTTTCAACGTACAATTCGGGTCGAGCGGTAt                                               >  1:829995/1‑62 (MQ=255)

                       tCGAGCTGCGCGTAAAAGCCGAGCAACTCCCCTTTCAACGTACAATTCGGGTCGAGCGGTATGCTTTtctc                                      >  1:1256375/1‑71 (MQ=255)

                        cGAGCTGCGCGTAAAAGCCGAGCAACTCCCCTTTCAACGTACAATTCGGGTCGAGCGGTATGCTTTtctc                                      <  1:2578387/70‑1 (MQ=255)

                          aGCTGCGCGTAAAAGCCGAGCAACTCCCCTTTCAACGTACAATTCGGGTCGAGCGGTATg                                              >  1:1552677/1‑60 (MQ=255)

                          aGCTGCGCGTAAAAGCCGAGCAACTCCCCTTTCAACGTACAATTCGGGTCGAGCGGTATGCTTTTCTCgag                                   <  1:2745835/71‑1 (MQ=255)

                          aGCTGCGCGTAAAAGCCGAGCAACTCCCCTTTCAACGTACAATTCGGGGCGAGCGGTATGCTTTTCTCgag                                   <  1:1776202/71‑1 (MQ=255)

                            cTGCGCGTAAAAGCCGAGCAACTCCCCTTTCAACGTACAATTCGGGTCGAGCgg                                                  <  1:970164/54‑1 (MQ=255)

                             tGCGCGTAAAAGCCGAGCAACTCCCCTTTCAACGTACAATTCgg                                                           >  1:584379/1‑44 (MQ=255)

                              gcgcGTAAAAGCCGAGCAACTCCCCTTTCAACGTACAATTCGGGTCGAGCGGTATGCTTTTCTCGAGAATa                               >  1:2190548/1‑71 (MQ=255)

                              gcgcGTAAAAGCCGAGCAACTCCCCTTTCAACGTAAAATTCGGGTCGAGCGGTATGCTTTtct                                       <  1:444231/63‑1 (MQ=255)

                                gcgTAAAAGCCGAGCAACTCCCCTTTCAACGTACAATTCGGGTCGAGCGGTATGCTTTTCTCg                                     >  1:2788701/1‑63 (MQ=255)

                                gcgTAAAAGCCGAGCAACTCCCCTTTCAACGTACAATTCGGGTCGAGCGGTATGCTTTTCTCGAGAATACt                             <  1:440084/71‑1 (MQ=255)

                                  gTAAAAGCCGAGCAACTCCCCTTTCAACGTACAATTCGGGTCGAGCGGTATGCTTTTCTCGAGAATACttt                           <  1:1705031/71‑1 (MQ=255)

                                    aaaaGCCGAGCAACTCCCCTTTCAACGTACAATTCGGGTCGAGCGGTATGCTTTTCTCg                                     <  1:2936456/59‑1 (MQ=255)

                                    aaaaGCCGAGCAACTCCCCTTTCAACGTACAATTCGGGTCGAGCGGTATGCTTTTCTCGAGAATACTTTg                          >  1:1056461/1‑70 (MQ=255)

                                     aaaGCCGAGCAACTCCCCTTTCAACGTACAATTCGGGTCGAGCGGTATGCTTTTCTCGAGAATACTTTGTa                        >  1:2512209/1‑71 (MQ=255)

                                      aaGCCGAGCAACTCCCCTTTCAACGTACAATTCGGGTCGAGCGGTATGCTTTtct                                       >  1:2579200/1‑55 (MQ=255)

                                      aaGCCGAGCAACTCCCCTTTCAACGTACAATTCGGGTCGAGCGGTATGCTTTTCTCgag                                   >  1:65161/1‑59 (MQ=255)

                                      aaGCCGAGCAACTCCCCTTTCAACGTACAATTCGGGTCGAGCGGTATGCTTTTCTCgag                                   >  1:2039665/1‑59 (MQ=255)

                                      aaGCCGAGCAACTCCCCTTTCAACGTACAATTCGGGTCGAGCGGTATGCTTTTCTCGAGAATACTTTggga                       >  1:1951065/1‑68 (MQ=255)

                                      aaGCCGAGCAACTCCCCTTTCAACGTACAATTCGGGGCGAGCGGTATGCTTTTCTCGAGAATACTTTGTAt                       <  1:1521175/71‑1 (MQ=255)

                                       aGCCGAGCAACTCCCCTTTCAACGTACAATTCGGGTCGAGCGGTATGCTTTTCTCGAGAATACTTTGTATc                      >  1:2680499/1‑71 (MQ=255)

                                          cGAGCATCTCCCCTTTCAACGTACAATTCGGGTCGAGCGGTATGCTTTTCTCGAGAATACTTTGt                         <  1:3105071/65‑1 (MQ=255)

                                          cGAGCAACTCCCCTTTCAACGTACAATTCGGGTCGAGCGGTATGCTTTTCTCGAGAATACTTTGt                         <  1:1763759/65‑1 (MQ=255)

                                             gCAACTCCCCTTTCAACGTACAATTCGGGTCGAGCGGTATGCTTTTCTCGAGAATACTTTGTATCTGAtt                 <  1:390816/70‑1 (MQ=255)

                                             gCAACTCCCCTTTCAACGTACAATTCGGGTCGAGCGGTATGCTTTTCTCGAGAATACTTTGTATCTGATTg                <  1:2381306/71‑1 (MQ=255)

                                               aaCTCCCCTTTCAACGTACAATTCGGGTCGAGCGGTATGCTTTTCTCGAGAATACttt                           <  1:2545138/58‑1 (MQ=255)

                                                    cccTTTCAACGTACAATTCGGGTCGAGCGGTATGCTTTTCTCGAGAATACTTTGTATCTGATTGGAAAc           <  1:1409277/69‑1 (MQ=255)

                                                    cccTTTCAACGTACAATTCGGGTCGAGCGGTATGCTTTTCTCGAGAATACTTTGTATCTGATTGGAAACAt         <  1:1599414/71‑1 (MQ=255)

                                                      cTTTCAACGTACAATTCGGGTCGAGCGGTATGCTTTTCTCGAGAATACTTTGTATCTGATTGGAAACATCt       >  1:261125/1‑71 (MQ=255)

                                                      cTTTCAACGTACAATTCGGGTCGAGCGGTATGCTTTTCTCGAGAATACTTTGTATCTGATTGGAAACATCt       >  1:1638439/1‑71 (MQ=255)

                                                        ttCAACGTACAATTCGGGTCGAGCGGTATGCTTTTCTCGAGAATACttt                           >  1:559986/1‑49 (MQ=255)

                                                        ttCAACGTACAATTCGGGTCGAGCGGTATGCTTTTCTCGAGAATACTTTGTATCTGATTGGaaa            >  1:1216814/1‑64 (MQ=255)

                                                         tCAACGTACAATTCGGGTCGAGCGGTATGCTTTtctc                                      >  1:3138131/1‑37 (MQ=255)

                                                         tCAACGTACAATTCGGGTCGAGCGGTATGCTTTtctc                                      >  1:2629678/1‑37 (MQ=255)

                                                         tCAACGTACAATTCGGGTCGAGCGGTATGCTTTtctc                                      >  1:2064026/1‑37 (MQ=255)

                                                            aCGTACAATTCGGGTCGAGCGGTATGCTTTTCTCGAGAATACTTTGTATCTGATTGGAAACATCTTTCTg  >  1:2630642/1‑70 (MQ=255)

                                                              gTACAATTCGGGTCGAGCGGTATGCTTTTCTCGAGAATACTTTGTATc                      <  1:2803031/48‑1 (MQ=255)

GGCTGGTATTACGACTTAAACCTTCGAGCTGCGCGTAAAAGCCGAGCAACTCCCCTTTCAACGTATAATTCGGGTCGAGCGGTATGCTTTTCTCGAGAATACTTTGTATCTGATTGGAAACATCTTTCTG  >  minE/1019732‑1019861

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