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
A1 F17 I0 R2	276	45.3	3729697	93.0%	3468618	60.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	1,521,063	C→T	67.7%	S108F (TCC→TTC)	yncB →	predicted oxidoreductase, Zn‑dependent and NAD(P)‑binding

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	1,521,063	0	C	T	67.7%	62.6 / 42.4	52	S108F (TCC→TTC)	yncB	predicted oxidoreductase, Zn‑dependent and NAD(P)‑binding
Reads supporting (aligned to +/- strand): ref base C (8/8); new base T (24/11); total (33/19)
Fisher's exact test for biased strand distribution p-value = 2.28e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GAATCATCCTGATTATCAGTCTGGCGACTGGGTGCTGGGCTACAGTGGATGGCAAGACTATGACATATCCAGTGGTGATGATCTGGTGAAACTTGGCGATCATCCGCAAAATCCATCGTGGTCGCTGGGTGTGCTA  >  W3110S.gb/1520995‑1521130

gAATCATCCTGATTATCAGTCTGGCGACTGGGTGCTGGGCTACAGTGGATGGCAAGACTATGACATATc                                                                     <  1:346564/69‑1 (MQ=255)

 aaTCATCCTGATTATCAGTCTGGCGACTGGGTGCTGGGCTACAGTGGATGGCAAGACTATGACATATc                                                                     <  1:63749/68‑1 (MQ=255)

        cTGATTATCAGTCTGGCGACTGGGTGCTGGGCTACAGTGGATGGCAAGACTATGACATATTCAgtggt                                                              <  1:2570832/68‑1 (MQ=255)

        cTGATTATCAGTCTGGCGACTGGGTGCTGGGCTACAGTGGATGGCAAGACTATGACATATTCAgtggt                                                              <  1:2392153/68‑1 (MQ=255)

        cTGATTATCAGTCTGGCGACTGGGTGCTGGGCTACAGTGGATGGCAAGACTATGACATATTCAgtggt                                                              <  1:288283/68‑1 (MQ=255)

        cTGATTATCAGTCTGGCGACTGGGTGCTGGGCTACAGTGGATGGCAAGACTATGACATATTCAgtggt                                                              <  1:1722737/68‑1 (MQ=255)

          gATTATCAGTCTGGCGACTGGGTGCTGGGCTACAGTGGATGGCAAGACTATGACATATCCAGTGGtgat                                                           <  1:1288696/69‑1 (MQ=255)

          gATTATCAGTCTGGCGACTGGGTGCTGGGCTACAGTGGATGGCAAGACTATGACATATCCAGTGGtgat                                                           <  1:2340861/69‑1 (MQ=255)

              aTCAGTCTGGCGACTGGGTGCTGGGCTACAGTGGATGGCAAGACTATGACATATTCAGTGGTGATGATc                                                       >  1:125341/1‑69 (MQ=255)

                     tGGCGACTGGGTGCTGGGCTACAGTGGATGGCAAGACTATGACATATTCAGTGGTGATGATCTGGTGaa                                                >  1:704593/1‑69 (MQ=255)

                     tGGCGACTGGGTGCTGGGCTACAGTGGATGGCAAGACTATGACATATTCAGTGGTGATGATCTGGTGaa                                                >  1:3368312/1‑69 (MQ=255)

                     tGGCGACTGGGTGCTGGGCTACAGTGGATGGCAAGACTATGACATATTCAGTGGTGATGATCTGGTGaa                                                >  1:1491571/1‑69 (MQ=255)

                         gACTGGGTGCTGGGCTACAGTGGATGGCAAGACTATGACATATTCAGTGGTGATGATCTGGTGAAAc                                              <  1:1837463/67‑1 (MQ=255)

                          aCTGGGTGCTGGGCTACAGTGGATGGCAAGACTATGACATATCCAGTGGTGATGATCTGGTGAAACTTg                                           >  1:610934/1‑69 (MQ=255)

                          aCTGGGTGCTGGGCTACAGTGGATGGCAAGACTATGACATATCCAGTGGTGATGATCTGGTGAAACTTg                                           >  1:599475/1‑69 (MQ=255)

                            tGGGTGCTGGGCTACAGTGGATGGCAAGACTATGACATATTCAgtggt                                                              >  1:3675309/1‑48 (MQ=255)

                            tGGGTGCTGGGCTACAGTGGATGGCAAGACTATGACATATTCAgtggt                                                              >  1:1684329/1‑48 (MQ=255)

                                     ggCTACAGTGGATGGCAAGACTATGACATATTCAGTGgaga                                                            >  1:347647/1‑41 (MQ=38)

                                     ggCTACAGTGGATGGCAAGACTATGACATATTCAGTGGtgat                                                           <  1:675247/42‑1 (MQ=255)

                                     ggCTACAGTGGATGGCAAGACTATGACATATTCAGTGGtgat                                                           >  1:2865535/1‑42 (MQ=255)

                                     ggCTACAGTGGATGGCAAGACTATGACATATTCAGTGGtgat                                                           <  1:1010299/42‑1 (MQ=255)

                                       cTACAGTGGATGGCAAGACTATGACATATTCAgtggt                                                              >  1:2920718/1‑37 (MQ=255)

                                       cTACAGTGGATGGCAAGACTATGACATATTCAgtggt                                                              >  1:2268704/1‑37 (MQ=255)

                                       cTACAGTGGATGGCAAGACTATGACATATTCAgtggt                                                              >  1:2849975/1‑37 (MQ=255)

                                       cTACAGTGGATGGCAAGACTATGACATATTCAGTGGTGATGATCTGGTGAAACTTGGCGATCATCCGCa                              <  1:296158/69‑1 (MQ=255)

                                       cTACAGTGGATGGCAAGACTATGACATATTCAGTGGTGATGATCTGGTGAAACTTGGCGATCATCCGCa                              <  1:2399332/69‑1 (MQ=255)

                                       atACAGTGGATGGCAAGACTATGACATATTCAgtggt                                                              >  1:575078/2‑37 (MQ=39)

                                        tACAGTGGATGGCAAGACTATGACATATTCAGTGGTGATGATCTGGTGAAACTTGGCGATCATCCGCaa                             <  1:3409420/69‑1 (MQ=255)

                                        tACAGTGGATGGCAAGACTATGACATATTCAGTGGTGATGATCTGGTGAAACTTGGCGATCATCCGCaa                             <  1:747639/69‑1 (MQ=255)

                                             tGGATGGCAAGACTATGACATATTCAGTGGTGATGATCTGGTGAAACTTGGc                                         >  1:1461609/1‑52 (MQ=255)

                                             tGGATGGCAAGACTATGACATATTCAGTGGTGATGATCTGGTGAAACTTGGCGATCATCCGCAAAATcc                        >  1:2852400/1‑69 (MQ=255)

                                             tGGATGGCAAGACTATGACATATTCAGTGGTGATGATCTGGTGAAACTTGGCGATCATCCGCAAAATcc                        >  1:1971074/1‑69 (MQ=255)

                                             tGGATGGCAAGACTATGACATATTCAGTGGTGATGATCTGGTGAAACTTGGCGATCATCCGCAAAATcc                        >  1:597153/1‑69 (MQ=255)

                                             tGGATGGCAAGACTATGACATATTCAGTGGTGATGATCTGGTGAAACTTGGCGATCATCCGCAAAATcc                        >  1:1247628/1‑69 (MQ=255)

                                             tGGATGGCAAGACTATGACATATACAGTGGTGATGATCTGGTGAAACTTGGCGATCATCCGCAAAATcc                        >  1:1054791/1‑69 (MQ=255)

                                               gATGGCGAGACTATGACATATCCAGTGGTGATGATCTGGTGAAACTTGGCGatc                                     >  1:2258028/1‑54 (MQ=255)

                                               gATGGCAAGACTATGACATATTCAGTGGTGATGATCTGGTGAAACTTGGCGATCATCCGCAAAATCCAt                      >  1:1308434/1‑69 (MQ=255)

                                               gATGGCAAGACTATGACATATTCAGTGGTGATGATCTGGTGAAACTTGGCGATCATCCGCAAAATCCAt                      >  1:497897/1‑69 (MQ=255)

                                               gATGGCAAGACTATGACATATCCAGTGGTGATGATCTGGTGAAACTTGGCGATCATCCGCAAAATCCAt                      >  1:2445296/1‑69 (MQ=255)

                                               gATGGCAAGACTATGACATATCCAGTGGTGATGATCTGGTGAAACTTGGCGATCATCCGCAAAATCCAt                      >  1:2055266/1‑69 (MQ=255)

                                                  ggCAAGACTATGACATATTCAGTGGTGATGATCTGGTGAAACTTGGCGATCATCCGCAAAATCCATCGt                   >  1:2382670/1‑69 (MQ=255)

                                                  ggCAAGACTATGACATATTCAGTGGTGATGATCTGGTGAAACTTGGCGATCATCCGCAAAATCCATCGt                   >  1:68388/1‑69 (MQ=255)

                                                  ggCAAGACTATGACATATCCAGTGGTGATGATCTGGTGAAACTTGGCGat                                      <  1:2826250/50‑1 (MQ=255)

                                                  ggCAAGACTATGACATATCCAGTGGTGATGATCTGGTGAAACTTGGCGat                                      <  1:3623258/50‑1 (MQ=255)

                                                  ggCAAGACTATGACATATCCAGTGGTGATGATCTGGTGAAACTTGGCGat                                      <  1:1519240/50‑1 (MQ=255)

                                                   gCAAGACTATGACATATCCAGTGGTGATGATCTGGTGAAACTTGGCGat                                      <  1:131922/49‑1 (MQ=255)

                                                         cTATGACATATTCAGTGGTGATGATCTGGTGAAACTTGGCGATCATCCGCAAAATCCATCGTGGTc               >  1:335596/1‑66 (MQ=255)

                                                         cTATGACATATTCAGTGGTGATGATCTGGTGAAACTTGGCGATCATCCGCAAAATCCATCGTGGTc               >  1:2636922/1‑66 (MQ=255)

                                                            tGACATATCCAGTGGTGATGATCTGGTGAAACTTGGCGATCATCCGCAAAATCCATCGTGGTc               <  1:3307748/63‑1 (MQ=255)

                                                            tGACATATCCAGTGGTGATGATCTGGTGAAACTTGGCGATCATCCGCAAAATCCATCGTGGTc               <  1:711017/63‑1 (MQ=255)

                                                              aCATATTCAGTGGTGATGATCTGGTGAAACTTGGCGATCATCCGCAAAATCCATCGTGGTCGCTGGgtg       >  1:2555422/1‑69 (MQ=255)

                                                                   tCCAGTGGTGATGATCTGGTGAAACTTGGCGATCATCCGCAAAATCCATCGTGGTCGCTGGGTGTGCTa  >  1:610170/1‑69 (MQ=255)

                                                                   tCCAGTGGTGATGATCTGGTGAAACTTGGCGATCATCCGCAAAATCCATCGTGGTCGCTGGGTGTGCTa  >  1:1273775/1‑69 (MQ=255)

                                                                   tCCAGTGGTGATGATCTGGTGAAACTTGGCGATCATCCGCAAAATCCATCGTGGTCGCTGGGTGTGCTa  >  1:102806/1‑69 (MQ=255)

GAATCATCCTGATTATCAGTCTGGCGACTGGGTGCTGGGCTACAGTGGATGGCAAGACTATGACATATCCAGTGGTGATGATCTGGTGAAACTTGGCGATCATCCGCAAAATCCATCGTGGTCGCTGGGTGTGCTA  >  W3110S.gb/1520995‑1521130

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